Use of trem-1 inhibitors for treatment, elimination and eradication of hiv-1 infection

ABSTRACT

Compounds, compositions, and methods of treatment and prevention of HIV, including HIV-1 and HIV-2, Dengue, and Chikungunya infection are disclosed. The compounds are TREM-1 inhibitors. Combinations of these TREM-1 inhibitors and additional antiretroviral compounds, such as NRTI, NNRTI, integrase inhibitors, entry inhibitors, protease inhibitors, JAK inhibitors, macrophage depleting agents, and the like, are also disclosed. In one embodiment, the combinations include a combination of adenine, cytosine, thymidine, and guanine nucleoside antiviral agents, optionally in further combination with at least one additional antiviral agent that works via a different mechanism than a nucleoside analog. This combination has the potential to eliminate the presence of HIV, Dengue, or Chikungunya virus in an infected patient.

BACKGROUND OF THE INVENTION

In 1983, the etiological cause of AIDS was determined to be the humanimmunodeficiency virus (HIV-1). In 1985, it was reported that thesynthetic nucleoside 3′-azido-3′-deoxythymidine (AZT) inhibited thereplication of human immunodeficiency virus. Since then, a number ofother synthetic nucleosides, including 2′,3′-dideoxyinosine (DDI),2′,3′-dideoxycytidine (DDC), 3′-deoxy-2′,3′-didehydrothymidine (D4T),((1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]-2-cyclopentene-1-methanolsulfate (ABC),cis-2-hydroxymethyl-5-(5-fluorocytosin-1-yl)-1,3-oxathiolane ((−)-FTC),and (−)-cis-2-hydroxymethyl-5-(cytosin-1-yl)-1,3-oxathiolane (3TC), havebeen proven to be effective against HIV-1. After cellularphosphorylation to the 5′-triphosphate by cellular kinases, thesesynthetic nucleosides are incorporated into a growing strand of viralDNA, causing chain termination due to the absence of the 3′-hydroxylgroup. They can also inhibit the viral enzyme reverse transcriptase.

Drug-resistant variants of HIV-1 can emerge after prolonged treatmentwith an antiviral agent. Drug resistance most typically occurs bymutation of a gene that encodes for an enzyme used in viral replication,and most typically in the case of HIV-1, reverse transcriptase,protease, or DNA polymerase. Recently, it has been demonstrated that theefficacy of a drug against HIV-1 infection can be prolonged, augmented,or restored by administering the compound in combination or alternationwith a second, and perhaps third, antiviral compound that induces adifferent mutation from that caused by the principle drug.Alternatively, the pharmacokinetics, biodistribution, or other parameterof the drug can be altered by such combination or alternation therapy.In general, combination therapy is typically preferred over alternationtherapy because it induces multiple simultaneous pressures on the virus.However, drug resistance can still emerge, and no effective cure has yetbeen identified, such that a patient can ultimately stop treatment.

Treatment for AIDS using attachment and fusion inhibitors as well asother antiviral drugs has been somewhat effective. Current clinicaltreatments for HIV-1 infections include triple drug combinations calledHighly Active Antiretroviral Therapy (“HAART”). HAART typically involvesvarious combinations of nucleoside reverse transcriptase inhibitors,non-nucleoside reverse transcriptase inhibitors, and HIV-1 proteaseinhibitors. In compliant patients, HAART is effective in reducingmortality and progression of HIV-1 infection to AIDS. However, thesemultidrug therapies do not eliminate HIV-1 and long-term treatment oftenresults in multidrug resistance. Also, many of these drugs are highlytoxic and/or require complicated dosing schedules that reduce complianceand limit efficacy. There is, therefore, a continuing need for thedevelopment of additional drugs for the prevention and treatment ofHIV-1 infection and AIDS.

It would be useful to have combination therapy that minimizes thevirological failure of patients taking conventional antiretroviraltherapy. It would also be useful to provide a therapy that can provide acure for HIV/AIDS, by destroying the virus altogether in all itsreservoirs.

It would also be useful to have a combination therapy that can inhibitthe detrimental hyper-inflammatory events caused by HIV-1 that are notcurrently addressed by existing antiviral agents.

It would further be useful clinically to have a combination therapy thatcan selectively and potently inhibit pro-inflammatory events inmonocytes/macrophages, a primary HIV-1 target cell and viral reservoir,which is currently unmet by existing antivirals.

It would also be useful to have a combination therapy that canselectively inhibit HIV-1 infection, activation, and cell death inHIV-target cells in the brain/central nervous system (CNS) as well asother viral reservoirs, which is a currently unmet need with existingantiretroviral agents.

The present invention provides such therapy, as well as methods oftreatment using the therapy.

SUMMARY OF THE INVENTION

Antiretroviral TREM-1 inhibitors, compositions including suchinhibitors, and methods for their use in treating HIV-1 and HIV-2infections, as well as other viruses that rely on cellular activation toreplicate in host cells, such as Dengue, Influenza, West Nile, andChikingunya virus infections, are provided.

The TREM-1 inhibitors can be administered in combination therapy, forexample, using JAK inhibitors, HAART, macrophage depletion agentsincluding but not limited to those of bisphosphonate classes, such asalendronate, Ibandronate, and clodronate, and other immunomodulatorbased agents such as dasatinib or imatinib, or PI3K/Akt inhibitors.

It is believed that this therapy, particularly when administered at anearly stage in the development of HIV-1 infection, has the possibilityof eliminating HIV-1 infection in a person. While not wishing to bebound to a particular theory, it is believed that the TREM-1 inhibitorsfunction in a way that is not likely to provoke resistance (i.e., doesnot involve the selective pressure that traditionally confersresistance, including direct inhibition of viral enzymes, orintroduction of modified bases in a way that would provoke enzymatic orviral mutations, as a direct function of alteration/inhibition of theviral replication cycle). Instead, TREM-1 inhibitors can conferinhibition of pro-HIV events such as inhibition of IL-6, TNF-α, IL-1α/β,and monocyte and macrophage activation such as CD14⁺/CD16⁺ monocytes,and sCD163 production. Inhibition of these events results in inhibitionof a pro-HIV environment, wherein the milieu of reducedmonocyte/macrophage activation conferred by TREM-1 inhibitors results ina microenvironment that is not supportive of productive viralreplication.

Further, due to this mechanism, which indirectly confers amicroenvironment non-supportive of productive viral replication, whenthe TREM-1 inhibitors are combined with different nucleosides containingall the possible bases (ACTG), optionally in the presence of additionalagents, the combination minimizes the ability of the virus to adapt itsreverse transcriptase and develop resistance to any class of nucleosideantiviral nucleosides (i.e., adenine, cytosine, thymidine, or guanine),because it would be susceptible to at least one of the other nucleosideantiviral agents that are present, and/or the additional non-NRTItherapeutic agent. Furthermore, hitting the same target such as theactive site of the HIV-1 polymerase with different bases allows completeand thorough chain termination of all the possible growing viral DNAchains. The use of an NNRTI in addition to the four differentnucleosides (ACTG analogs) can be even more effective, since NNRTI bindto the HIV-polymerase and cause the enzyme to change conformationpreventing chain elogation by natural nucleosides interacting in theactive site of the enzyme.

In any of these embodiments, additional therapeutic agents can be usedin combination with these agents, particularly including agents with adifferent mode of attack. Such agents include but are not limited to:antivirals, such as cytokines, e.g., rIFN alpha, rIFN beta, rIFN gamma;amphotericin B as a lipid-binding molecule with anti-HIV activity; aspecific viral mutagenic agent (e.g., ribavirin), an HIV-1 VIFinhibitor, and an inhibitor of glycoprotein processing. Representativeanti-TNF-α therapies include, but are not limited to, Infliximab(Remicade), adalimumab (Humira), certolizumab pegol (Cimzia), andgolimumab (Simponi), alone or with a circulating receptor fusion proteinsuch as etanercept (Enbrel).

When administered in combination, the agents can be administered in asingle or in multiple dosage forms. In some embodiments, some of theantiviral agents are orally administered, whereas other antiviral agentsare administered by injection, which can occur at around the same time,or at different times.

The compounds can be used in different ways to treat or prevent HIV,and, in one embodiment, to cure an HIV infection. The inventionencompasses combinations of the two types of antiviral agents, orpharmaceutically acceptable derivatives thereof, that are synergistic,i.e., better than either agent or therapy alone.

In one embodiment, a combination of a TREM-1 inhibitor as describedherein, a macrophage depleting agent (e.g., clodronate-loaded liposomesor bisphosphonate class agents loaded in either liposomes or variousnanoparticle formulations, gadolinium chloride (GdCl)), plus HAARTtherapy is used.

In another embodiment, a combination of a histone deacetylase inhibitor(HDAC inhibitor) or interleukin 7 (IL-7) and HAART and a TREM-1inhibitor is used.

In another embodiment, the TREM-1 inhibitors are administered to apatient before, during, or after administration of a vaccine or animmunomodulatory agent, such as Jak inhibitors, PI3K inhibitors, ordasatinib/imatinib.

Combinations of these approaches can also be used.

The antiviral combinations described herein provide means of treatmentwhich can not only reduce the effective dose of the individual drugsrequired for antiviral activity, thereby reducing toxicity, but can alsoimprove their absolute antiviral effect, as a result of attacking thevirus through multiple mechanisms. That is, various combinationsdescribed herein are useful because their synergistic actions permit theuse of less drug, and/or increase the efficacy of the drugs when usedtogether in the same amount as when used alone.

The use of TREM-1 inhibitors, alone or in combination, provides a meansfor circumventing the development of viral resistance, thereby providingthe clinician with a more efficacious treatment.

The disclosed TREM-1 inhibitors, used alone or in combination or inalternation therapies, are useful in the prevention and treatment ofHIV-1 infections and other related conditions such as AIDS-relatedcomplex (ARC), persistent generalized lymphadenopathy (PGL),AIDS-related neurological conditions, anti-HIV antibody positive andHIV-positive conditions, Kaposi's sarcoma, thrombocytopenia purpurea andopportunistic infections. In addition, these compounds or formulationscan be used prophylactically to prevent or retard the progression ofclinical illness in individuals who are anti-HIV antibody or HIV-antigenpositive or who have been exposed to HIV. The therapy can be also usedto treat other viral infections, such as HIV-2, Dengue and Chikungunyavirus.

HIV-2 presents with significant similarities to HIV-1 relative toimmunomodulatory events that are key to productive viral replication.These events are similar within HIV-1 and HIV-2, whereinpro-inflammatory cytokines, upregulation of activation markers,trafficking across and within the blood-brain-barrier of infected cells,and systemic hyperactivation across and within various microenvironmentsexists for both viruses.

As discussed herein, TREM-1 inhibitors can be useful for both treatment,prophylaxis, and eradication of both HIV-1 and HIV-2. For Chikungunyavirus, the pathology of this virus is hyper-inflammatory cytokines,including IL-6, TNF-α, CRP, IL-1α/β, and others. Chikungunya virusresults in a severe rheumatoid arthritis pathology systemically, and itwould be useful for a drug to inhibit these events specifically andpotently, as do TREM-1 inhibitors. Monocytes/macrophages are a majortarget cell of Chikungunya virus, and TREM-1 inhibitors inhibit theabove described pro-inflammatory cytokines produced bymonocytes/macrophages specifically. Inhibition of these cytokines cantreat Chikungunya virus infection. Inhibition of these cytokines caneradicate Chikungunya virus infection, or be used herein to provideprophylaxis for Chikungunya virus infection.

Dengue virus is known to infect megakaryocytes (as well as other cellssuch as hepatocytes) and any modulation in these cells to reduceinflammation could be beneficial.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a chart showing extracellular tissue necrosis factor-alpha(TNF-α) production in acutely infected resting or activated macrophagesor constitutively exposed to lipopolysaccharide (LPS), shown in terms ofpg/ml extracellular TNF-α. FIG. 2 is a chart showing the potency andtoxicity of JAK inhibitors Tofacitinib or Jakafi versus FDA approvedcontrol AZT in acutely infected resting macrophages (MØ), as well as inperipheral blood mononuclear (PBM) cells. Median effective antiviralconcentration (EC₅₀) data (potency) is shown in terms of μMconcentration of the compounds. The IC₅₀ values (toxicity) (μM) are alsoshown in PBM, MØ cells, CEM cells, and Vero cells.

FIGS. 3A and 3B show the antiviral potency for co-administration ofruxolitinib and tofacitinib in primary human lymphocytes (FIG. 3A) andmacrophages (FIG. 3B, in terms of cell viability (%) versus M drug inmedium.

FIGS. 4A-D are charts showing the effect of Jak inhibitors on theproliferation and viability of PHA or PHA+IL-2 stimulated primary human,in terms of cell count X 10⁻⁶ vs. concentration of Jak inhibitor (M).For PHA stimulated lymphocytes, viability and proliferation were notsignificantly different than that of cells exposed to media alone forall concentrations of either ruxolitinib or tofacitinib (FIG. 4A, FIG.4C). For PHA+IL-2 stimulated lymphocytes, viability was notsignificantly different than that of cells exposed to media alone forall concentrations of either ruxolitinib (dotted line with squares) ortofacitinib (light gray line with diamonds) (FIG. 4B), howeverproliferation was significantly inhibited by 1 μM of ruxolitinib ortofacitinib (FIG. 4D).

FIGS. 5A and 5B are charts showing the results of exposure of primaryhuman monocytes to replication competent M-R5 HIV-1 BaL for 5 days priorto quantification of HIV-induced activation (CD14+/CD16⁺ monocytes;tandem two color FACS). FIG. 5A shows that HIV infection is associatedwith an increase in the number of activated monocytes. FIG. 5B showsthat following administration of TREM-1 peptide, the number of activatedmonocytes was lower. The assay represents three independent donorsconducted with duplicates. Data are mean and standard deviations, *indicates significant reduction versus BaL infected, no drug control(one-way ANOVA).

FIGS. 6A-6D are charts showing the percentage of positive cells (%) inthe presence or absence of various concentrations of TREM-1 peptide(μM). Following treatment of primary human macrophages with replicationcompetent M-R5 HIV-1 BaL for 5 days, the TREM-1 peptide significantlyreduced HIV-induced activation in primary human macrophages, as shownwith HIV-1 induced activation markers HLA-DR (FIG. 6A), CCR5 (FIG. 6B),and CD163 (FIG. 6C); * one way ANOVA). TREM-1 peptide does not reduceCD4 expression (FIG. 6D), demonstrating that CD4 receptorexpression-mediated innate and adaptive immunity is not altered. HIV-1BaL significantly increases activation markers CD163, CCR5, and CD163versus no virus control (**; one-way ANOVA). Data are mean and standarddeviation for three independent donors conducted in duplicates.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is directed to compounds, compositions and methodsfor treating viral infections, such as HIV infections, including HIV-1and HIV-2 infections, as well as other viruses that rely on cellularactivation to replicate in host cells, such as Dengue, Influenza, WestNile, and Chikingunya virus infections. In one embodiment, the compoundsare TREM-1 inhibitors, which can be administered alone, or incombination or alternation with JAK inhibitors, such as heteroarylsubstituted pyrrolo[2,3-b]pyridines and heteroaryl substitutedpyrrolo[2,3-b]pyrimidines that modulate the activity of Janus kinases(JAK inhibitors), HAART therapy, or other anti-HIV therapies.

The various embodiments of the invention are described in more detailbelow, and will be better understood with reference to the followingnon-limiting definitions.

Definitions

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as is commonly understood by one of ordinary skillin the art. All patents, applications, published applications and otherpublications referenced herein are incorporated by reference in theirentirety unless stated otherwise. In the event that there are aplurality of definitions for a term herein, those in this sectionprevail unless stated otherwise.

As used herein, any “R” group(s) such as, without limitation, R¹,R^(1a), R^(1b), R^(c), and R^(1d) represent substituents that can beattached to the indicated atom. A non-limiting list of R groups include,but are not limited to, hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl,cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl,heteroaralkyl, (heteroalicyclyl)alkyl, hydroxy, protected hydroxy,alkoxy, aryloxy, acyl, ester, mercapto, cyano, halogen, thiocarbonyl,O-carbamyl, N-carbamyl, O-thiocarbamyl, N-thiocarbamyl, C-amido,N-amido, S-sulfonamido, N-sulfonamide, C-carboxy, protected C-carboxy,O-carboxy, isocyanato, thiocyanato, isothiocyanato, nitro, silyl,sulfenyl, sulfinyl, sulfonyl, haloalkyl, haloalkoxy,trihalomethanesulfonyl, trihalomethanesulfonamido, and amino, includingmono- and di-substituted amino groups, and the protected derivativesthereof. An R group may be substituted or unsubstituted. If two “R”groups are covalently bonded to the same atom or to adjacent atoms, thenthey may be “taken together” as defined herein to form a cycloalkyl,cycloalkenyl, cycloalkynyl, aryl, heteroaryl or heteroalicyclyl group.For example, without limitation, if R′ and R″ of an NR′R″ group areindicated to be “taken together”, it means that they are covalentlybonded to one another at their terminal atoms to form a ring thatincludes the nitrogen:

Whenever a group is described as being “optionally substituted” thatgroup may be unsubstituted or substituted with one or more of theindicated substituents. Likewise, when a group is described as being“unsubstituted or substituted” if substituted, the substituent may beselected from one or more the indicated substituents. If no substituentsare indicated, it is meant that the indicated “optionally substituted”or “substituted” group may be substituted with one or more group(s)individually and independently selected from alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl,hydroxy, protected hydroxyl, alkoxy, aryloxy, acyl, ester, mercapto,alkylthio, arylthio, cyano, halogen, thiocarbonyl, O-carbamyl,N-carbamyl, O-thiocarbamyl, N-thiocarbamyl, C-amido, N-amido,S-sulfonamido, N-sulfonamido, C-carboxy, protected C-carboxy, O-carboxy,isocyanato, thiocyanato, isothiocyanato, nitro, silyl, sulfenyl,sulfinyl, sulfonyl, haloalkyl, haloalkoxy, trihalomethanesulfonyl,trihalomethanesulfonamido, and amino, including mono- and di-substitutedamino groups, and the protected derivatives thereof. Each of thesesubstituents can be further substituted.

As used herein, “C_(a) to C_(b)” in which “a” and “b” are integers referto the number of carbon atoms in an alkyl, alkenyl or alkynyl group, orthe number of carbon atoms in the ring of a cycloalkyl, cycloalkenyl,cycloalkynyl, aryl, heteroaryl or heteroalicyclyl group. That is, thealkyl, alkenyl, alkynyl, ring of the cycloalkyl, ring of thecycloalkenyl, ring of the cycloalkynyl, ring of the aryl, ring of theheteroaryl or ring of the heteroalicyclyl can contain from “a” to “b”,inclusive, carbon atoms. Thus, for example, a “C₁ to C₄ alkyl” grouprefers to all alkyl groups having from 1 to 4 carbons, that is, CH₃—,CH₃CH₂—, CH₃CH₂CH₂—, (CH₃)₂CH—, CH₃CH₂CH₂CH₂—, CH₃CH₂CH(CH₃)— and(CH₃)₃C—. If no “a” and “b” are designated with regard to an alkyl,alkenyl, alkynyl, cycloalkyl cycloalkenyl, cycloalkynyl, aryl,heteroaryl or heteroalicyclyl group, the broadest range described inthese definitions is to be assumed.

As used herein, the term “alkyl” can be straight or branched hydrocarbonchains that comprise a fully saturated (no double or triple bonds)hydrocarbon group. The alkyl group may have 1 to 20 carbon atoms(whenever it appears herein, a numerical range such as “1 to 20” refersto each integer in the given range; e.g., “1 to 20 carbon atoms” meansthat the alkyl group may consist of 1 carbon atom, 2 carbon atoms, 3carbon atoms, etc., up to and including 20 carbon atoms, although thepresent definition also covers the occurrence of the term “alkyl” whereno numerical range is designated). The alkyl group may also be a mediumsize alkyl having 1 to 10 carbon atoms. The alkyl group can also be alower alkyl having 1 to 6 carbon atoms. The alkyl group of the compoundsmay be designated as “C₁-C₆ alkyl” or similar designations. By way ofexample only, “C₁-C₄ alkyl” indicates that there are one to four carbonatoms in the alkyl chain, i.e., the alkyl chain is selected from methyl,ethyl, propyl, iso-propyl, n-butyl, iso-butyl, sec-butyl, and t-butyl.By way of example only, “C₁-C₆ alkyl” indicates that there are one tosix carbon atoms in the alkyl chain. Typical alkyl groups include, butare in no way limited to, methyl, ethyl, propyl, isopropyl, butyl,isobutyl, tertiary butyl, pentyl, hexyl, and the like. The alkyl groupmay be substituted or unsubstituted.

As used herein, “alkenyl” refers to an alkyl group that contains in thestraight or branched hydrocarbon chain one or more double bonds. Analkenyl group may be unsubstituted or substituted.

As used herein, “alkynyl” refers to an alkyl group that contains in thestraight or branched hydrocarbon chain one or more triple bonds. Analkynyl group may be unsubstituted or substituted.

As used herein, the term “alkoxy” includes O-alkyl groups wherein“alkyl” is defined above. As used herein, “cycloalkyl” refers to acompletely saturated (no double or triple bonds) mono- or multi-cyclichydrocarbon ring system. When composed of two or more rings, the ringsmay be joined together in a fused fashion. Cycloalkyl groups can contain3 to 10 atoms in the ring(s) or 3 to 8 atoms in the ring(s). Acycloalkyl group may be unsubstituted or substituted. Typical cycloalkylgroups include, but are in no way limited to, cyclopropyl, cyclobutyl,cyclopentyl, cyclohexyl, and the like.

As used herein, “cycloalkenyl” refers to a mono- or multi-cyclichydrocarbon ring system that contains one or more double bonds in atleast one ring; although, if there is more than one, the double bondscannot form a fully delocalized pi-electron system throughout all therings (otherwise the group would be “aryl,” as defined herein). Whencomposed of two or more rings, the rings may be connected together in afused fashion. A cycloalkenyl group may be unsubstituted or substituted.

As used herein, “cycloalkynyl” refers to a mono- or multi-cyclichydrocarbon ring system that contains one or more triple bonds in atleast one ring. Pf there is more than one triple bond, the triple bondscannot form a fully delocalized pi-electron system throughout all therings. When composed of two or more rings, the rings may be joinedtogether in a fused fashion. A cycloalkynyl group may be unsubstitutedor substituted.

As used herein, “aryl” refers to a carbocyclic (all carbon) monocyclicor multicyclic aromatic ring system (including fused ring systems wheretwo carbocyclic rings share a chemical bond) that has a fullydelocalized pi-electron system throughout all the rings. The number ofcarbon atoms in an aryl group can vary. For example, the aryl group is aC₆₋₁₄ aryl group, a C₆₋₁₀ aryl group, or a C₆ aryl group. Examples ofaryl groups include, but are not limited to, benzene, naphthalene andazulene. An aryl group may be substituted or unsubstituted.

As used herein, “heteroaryl” refers to a monocyclic or multicyclicaromatic ring system (a ring system with fully delocalized pi-electronsystem) that contain(s) one or more heteroatoms, that is, an elementother than carbon, including but not limited to, nitrogen, oxygen andsulfur. The number of atoms in the ring(s) of a heteroaryl group canvary. For example, the heteroaryl group can contain 4 to 14 atoms in thering(s), 5 to 10 atoms in the ring(s) or 5 to 6 atoms in the ring(s).Furthermore, the term “heteroaryl” includes fused ring systems where tworings, such as at least one aryl ring and at least one heteroaryl ring,or at least two heteroaryl rings, share at least one chemical bond.Examples of heteroaryl rings include, but are not limited to, furan,furazan, thiophene, benzothiophene, phthalazine, pyrrole, oxazole,benzoxazole, 1,2,3-oxadiazole, 1,2,4-oxadiazole, thiazole,1,2,3-thiadiazole, 1,2,4-thiadiazole, benzothiazole, imidazole,benzimidazole, indole, indazole, pyrazole, benzopyrazole, isoxazole,benzoisoxazole, isothiazole, triazole, benzotriazole, thiadiazole,tetrazole, pyridine, pyridazine, pyrimidine, pyrazine, purine,pteridine, quinoline, isoquinoline, quinazoline, quinoxaline, cinnoline,and triazine. A heteroaryl group may be substituted or unsubstituted.

As used herein, “heteroalicyclic” or “heteroalicyclyl” refers to three-,four-, five-, six-, seven-, eight-, nine-, ten-, up to 18-memberedmonocyclic, bicyclic, and tricyclic ring system wherein carbon atomstogether with from 1 to 5 heteroatoms constitute said ring system. Aheterocycle may optionally contain one or more unsaturated bondssituated in such a way, however, that a fully delocalized pi-electronsystem does not occur throughout all the rings. The heteroatoms areindependently selected from oxygen, sulfur, and nitrogen. A heterocyclemay further contain one or more carbonyl or thiocarbonylfunctionalities, so as to make the definition include oxo-systems andthio-systems such as lactams, lactones, cyclic imides, cyclicthioimides, cyclic carbamates, and the like. When composed of two ormore rings, the rings may be joined together in a fused fashion.Additionally, any nitrogens in a heteroalicyclic may be quaternized.Heteroalicyclyl or heteroalicyclic groups may be unsubstituted orsubstituted. Examples of such “heteroalicyclic” or “heteroalicyclyl”groups include but are not limited to, 1,3-dioxin, 1,3-dioxane,1,4-dioxane, 1,2-dioxolane, 1,3-dioxolane, 1,4-dioxolane, 1,3-oxathiane,1,4-oxathiin, 1,3-oxathiolane, 1,3-dithiole, 1,3-dithiolane,1,4-oxathiane, tetrahydro-1,4-thiazine, 2H-1,2-oxazine, maleimide,succinimide, barbituric acid, thiobarbituric acid, dioxopiperazine,hydantoin, dihydrouracil, trioxane, hexahydro-1,3,5-triazine,imidazoline, imidazolidine, isoxazoline, isoxazolidine, oxazoline,oxazolidine, oxazolidinone, thiazoline, thiazolidine, morpholine,oxirane, piperidine N-Oxide, piperidine, piperazine, pyrrolidine,pyrrolidone, pyrrolidione, A-piperidone, pyrazoline, pyrazolidine,2-oxopyrrolidine, tetrahydropyran, 4H-pyran, tetrahydrothiopyran,thiamorpholine, thiamorpholine sulfoxide, thiamorpholine sulfone, andtheir benzo-fused analogs (e.g., benzimidazolidinone,tetrahydroquinoline, 3,4-methylenedioxyphenyl).

An “aralkyl” is an aryl group connected, as a substituent, via a loweralkylene group. The lower alkylene and aryl group of an aralkyl may besubstituted or unsubstituted. Examples include but are not limited tobenzyl, substituted benzyl, 2-phenylalkyl, 3-phenylalkyl, andnaphtylalkyl.

A “heteroaralkyl” is heteroaryl group connected, as a substituent, via alower alkylene group. The lower alkylene and heteroaryl group ofheteroaralkyl may be substituted or unsubstituted. Examples include butare not limited to 2-thienylalkyl, 3-thienylalkyl, furylalkyl,thienylalkyl, pyrrolylalkyl, pyridylalkyl, isoxazolylalkyl, andimidazolylalkyl, and their substituted as well as benzo-fused analogs.

A “(heteroalicyclyl)alkyl” is a heterocyclic or a heteroalicyclylicgroup connected, as a substituent, via a lower alkylene group. The loweralkylene and heterocyclic or a heterocyclyl of a (heteroalicyclyl)alkylmay be substituted or unsubstituted. Examples include but are notlimited tetrahydro-2H-pyran-4-yl)methyl, (piperidin-4-yl)ethyl,(piperidin-4-yl)propyl, (tetrahydro-2H-thiopyran-4-yl)methyl, and(1,3-thiazinan-4-yl)methyl.

“Lower alkylene groups” are straight-chained tethering groups, formingbonds to connect molecular fragments via their terminal carbon atoms.Examples include but are not limited to methylene (—CH₂—), ethylene(—CH₂CH₂—), propylene (—CH₂CH₂CH₂—), and butylene (—CH₂CH₂CH₂CH₂—). Alower alkylene group may be substituted or unsubstituted.

As used herein, “alkoxy” refers to the formula —OR wherein R is analkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl isdefined as above. Examples of include methoxy, ethoxy, n-propoxy,1-methylethoxy (isopropoxy), n-butoxy, iso-butoxy, sec-butoxy,tert-butoxy, phenoxy and the like. An alkoxy may be substituted orunsubstituted.

As used herein, “acyl” refers to a hydrogen, alkyl, alkenyl, alkynyl, oraryl connected, as substituents, via a carbonyl group. Examples includeformyl, acetyl, propanoyl, benzoyl, and acryl. An acyl may besubstituted or unsubstituted.

As used herein, “hydroxyalkyl” refers to an alkyl group in which one ormore of the hydrogen atoms are replaced by hydroxy group. Examples ofhydroxyalkyl groups include but are not limited to, 2-hydroxyethyl,3-hydroxypropyl, 2-hydroxypropyl, and 2,2-dihydroxyethyl. A hydroxyalkylmay be substituted or unsubstituted.

As used herein, “haloalkyl” refers to an alkyl group in which one ormore of the hydrogen atoms are replaced by halogen (e.g.,mono-haloalkyl, di-haloalkyl and tri-haloalkyl). Such groups include butare not limited to, chloromethyl, fluoromethyl, difluoromethyl,trifluoromethyl and 1-chloro-2-fluoromethyl, 2-fluoroisobutyl. Ahaloalkyl may be substituted or unsubstituted.

As used herein, “haloalkoxy” refers to an alkoxy group in which one ormore of the hydrogen atoms are replaced by halogen (e.g.,mono-haloalkoxy, di-haloalkoxy and tri-haloalkoxy). Such groups includebut are not limited to, chloromethoxy, fluoromethoxy, difluoromethoxy,trifluoromethoxy and 1-chloro-2-fluoromethoxy, 2-fluoroisobutoxy. Ahaloalkoxy may be substituted or unsubstituted.

A “sulfenyl” group refers to an “—SR” group in which R is hydrogen,alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl. Asulfenyl may be substituted or unsubstituted.

A “sulfinyl” group refers to an “—S(═O)—R” group in which R is the sameas defined with respect to sulfenyl. A sulfinyl may be substituted orunsubstituted.

A “sulfonyl” group refers to an “SO₂R” group in which R is the same asdefined with respect to sulfenyl. A sulfonyl may be substituted orunsubstituted.

An “O-carboxy” group refers to a “RC(═O)O—” group in which R ishydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl,cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, or(heteroalicyclyl)alkyl, as defined herein. An O-carboxy may besubstituted or unsubstituted.

The terms “ester” and “C-carboxy” refer to a “—C(═O)OR” group in which Ris the same as defined with respect to O-carboxy. An ester and C-carboxymay be substituted or unsubstituted.

A “thiocarbonyl” group refers to a “—C(═S)R” group in which R is thesame as defined with respect to O-carboxy. A thiocarbonyl may besubstituted or unsubstituted.

A “trihalomethanesulfonyl” group refers to an “X₃CSO₂—” group wherein Xis a halogen.

A “trihalomethanesulfonamido” group refers to an “X₃CS(O)₂RN—” groupwherein X is a halogen and R defined with respect to O-carboxy.

The term “amino” as used herein refers to a —NH₂ group.

As used herein, the term “hydroxy” refers to a —OH group.

A “cyano” group refers to a “—CN” group.

The term “azido” as used herein refers to a —N₃ group.

An “isocyanato” group refers to a “—NCO” group.

A “thiocyanato” group refers to a “—CNS” group.

An “isothiocyanato” group refers to an “—NCS” group.

A “mercapto” group refers to an “—SH” group.

A “carbonyl” group refers to a C═O group.

An “S-sulfonamido” group refers to a “—SO₁NR_(A)R_(B)” group in whichR_(A) and R_(B) are the same as R defined with respect to O-carboxy. AnS-sulfonamido may be substituted or unsubstituted.

An “N-sulfonamido” group refers to a “R_(B)SO₂N(R_(A))—” group in whichR_(A) and R_(B) are the same as R defined with respect to O-carboxy. AN-sulfonamido may be substituted or unsubstituted.

An “O-carbamyl” group refers to a “—OC(═O)NR_(A)R_(B)” group in whichR_(A) and R_(B) are the same as R defined with respect to O-carboxy. AnO-carbamyl may be substituted or unsubstituted.

An “N-carbamyl” group refers to an “R_(B)OC(═O)NR_(A)—” group in whichR_(A) and R_(B) are the same as R defined with respect to O-carboxy. AnN-carbamyl may be substituted or unsubstituted.

An “O-thiocarbamyl” group refers to a “—OC(═S)—NR_(A)R_(B)” group inwhich R_(A) and R_(B) are the same as R defined with respect toO-carboxy. An O-thiocarbamyl may be substituted or unsubstituted.

An “N-thiocarbamyl” group refers to an “R_(B)OC(═S)NR_(A)—” group inwhich R_(A) and R_(B) are the same as R defined with respect toO-carboxy. An N-thiocarbamyl may be substituted or unsubstituted.

A “C-amido” group refers to a “—C(═O)NR_(A)R_(B)” group in which R_(A)and R_(B) are the same as R defined with respect to O-carboxy. A C-amidocan be substituted or unsubstituted.

An “N-amido” group refers to a “R_(B)C(═O)NR_(A)—” group in which R_(A)and R_(B) are the same as R defined with respect to O-carboxy. AnN-amido can be substituted or unsubstituted.

As used herein, “organylcarbonyl” refers to a group of the formula—C(═O)R′wherein R′ can be alkyl, alkenyl, alkynyl, cycloalkyl,cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl,or (heteroalicyclyl)alkyl. An organylcarbonyl can be substituted orunsubstituted.

The term “alkoxycarbonyl” as used herein refers to a group of theformula —C(═O)OR′, wherein R′ is the same as defined with respect toorganylcarbonyl. An alkoxycarbonyl can be substituted or unsubstituted.

As used herein, “organylaminocarbonyl” refers to a group of the formulaC(═O)NR′R″ wherein R′ and R″ are independently selected from the samesubstituents as defined with respect to organylcarbonyl. Anorganylaminocarbonyl can be substituted or unsubstituted.

As used herein, the term “levulinoyl” refers to a —C(═O)CH₂CH₂C(═O)CH₃group.

The term “halogen atom,” as used herein, means any one of theradio-stable atoms of column 7 of the Periodic Table of the Elements,i.e., fluorine, chlorine, bromine, or iodine, with fluorine and chlorinebeing preferred.

Where the numbers of substituents is not specified (e.g. haloalkyl),there may be one or more substituents present. For example “haloalkyl”may include one or more of the same or different halogens. As anotherexample, “C₁-C₃ alkoxyphenyl” may include one or more of the same ordifferent alkoxy groups containing one, two or three atoms.

As used herein, the term “nucleoside” refers to a compound composed ofany pentose or modified pentose moiety attached to a specific portion ofa heterocyclic base, tautomer, or derivative thereof such as the9-position of a purine, 1-position of a pyrimidine, or an equivalentposition of a heterocyclic base derivative. Examples include, but arenot limited to, a ribonucleoside comprising a ribose moiety and adeoxyribonucleoside comprising a deoxyribose moiety, and in someinstances, the nucleoside is a nucleoside drug analog. As used herein,the term “nucleoside drug analog” refers to a compound composed of anucleoside that has therapeutic activity, such as antiviral,antineoplastic, anti-parasitic and/or antibacterial activity.

As used herein, the term “nucleotide” refers to a nucleoside having aphosphate ester substituted on the 5′-position or an equivalent positionof a nucleoside derivative.

As used herein, the term “heterocyclic base” refers to a purine, apyrimidine and derivatives thereof. The term “purine” refers to asubstituted purine, its tautomers and analogs thereof. Similarly, theterm “pyrimidine” refers to a substituted pyrimidine, its tautomers andanalogs thereof. Examples of purines include, but are not limited to,purine, adenine, guanine, hypoxanthine, xanthine, theobromine, caffeine,uric acid and isoguanine. Examples of pyrimidines include, but are notlimited to, cytosine, thymine, uracil, and derivatives thereof. Anexample of an analog of a purine is 1,2,4-triazole-3-carboxamide.

Other non-limiting examples of heterocyclic bases include diaminopurine,8-oxo-N⁶-methyladenine, 7-deazaxanthine, 7-deazaguanine,N⁴,N⁴-ethanocytosin, N⁶,N⁶-ethano-2,6-diaminopurine, 5-methylcytosine,5-fluorouracil, 5-bromouracil, pseudoisocytosine, isocytosine,isoguanine, and other heterocyclic bases described in U.S. Pat. Nos.5,432,272 and 7,125,855, which are incorporated herein by reference forthe limited purpose of disclosing additional heterocyclic bases.

The term “—O-linked amino acid” refers to an amino acid that is attachedto the indicated moiety via its main-chain carboxyl function group. Whenthe amino acid is attached, the hydrogen that is part of the —OH portionof the carboxyl function group is not present and the amino acid isattached via the remaining oxygen. An —O-linked amino acid can beprotected at any nitrogen group that is present on the amino acid. Forexample, an —O-linked amino acid can contain an amide or a carbamategroup. Suitable amino acid protecting groups include, but are notlimited to, carbobenzyloxy (Cbz), p-methoxybenzyl carbonyl (Moz orMeOZ), tert-butyloxycarbonyl (BOC), 9-fluorenylmethyloxycarbonyl (FMOC),benzyl (Bn), p-methoxybenzyl (PMB), 3,4-dimethoxybenzyl (DMPM), andtosyl (Ts) groups. The term “—N-linked amino acid” refers to an aminoacid that is attached to the indicated moiety via its main-chain aminoor mono-substituted amino group. When the amino acid is attached in an—N-linked amino acid, one of the hydrogens that is part of themain-chain amino or mono-substituted amino group is not present and theamino acid is attached via the nitrogen. An —N-linked amino acid can beprotected at any hydroxyl or carboxyl group that is present on the aminoacid. For example, an —N-linked amino acid can contain an ester or anether group. Suitable amino acid protecting groups include, but are notlimited to, methyl esters, ethyl esters, propyl esters, benzyl esters,tert-butyl esters, silyl esters, orthoesters, and oxazoline. As usedherein, the term “amino acid” refers to any amino acid (both standardand non-standard amino acids), including, but limited to, α-amino acidsβ-amino acids, γ-amino acids and δ-amino acids. Examples of suitableamino acids, include, but are not limited to, alanine, asparagine,aspartate, cysteine, glutamate, glutamine, glycine, proline, serine,tyrosine, arginine, histidine, isoleucine, leucine, lysine, methionine,phenylalanine, threonine, tryptophan and valine.

The terms “derivative,” “variant,” or other similar terms refer to acompound that is an analog of the other compound.

The terms “protecting group” and “protecting groups” as used hereinrefer to any atom or group of atoms that is added to a molecule in orderto prevent existing groups in the molecule from undergoing unwantedchemical reactions. Examples of protecting group moieties are describedin T. W Greene and P. G. M. Wuts, Protective Groups in OrganicSynthesis, 3. Ed. John Wiley & Sons (1999), and in J. F. W. McOmie,Protective Groups in Organic Chemistry Plenum Press (1973), both ofwhich are hereby incorporated by reference for the limited purpose ofdisclosing suitable protecting groups The protecting group moiety may bechosen in such a way, that they are stable to certain reactionconditions and readily removed at a convenient stage using methodologyknown from the art. A non-limiting list of protecting groups includebenzyl, substituted benzyl; alkylcarbonyls (e g., t-butoxycarbonyl(BOC)); arylalkylcarbonyls (e.g., benzyloxycarbonyl, benzoyl),substituted methyl ether (e.g. methoxymethyl ether); substituted ethylether, a substituted benzyl ether; tetrahydropyranyl ether; silyl ethers(e g, titmethylsilyl, tnethylsilyl, tnisopropylsilyl,t-butyldimethylsilyl, or t-butyldiphenylsilyl), esters (e.g. benzoateester), carbonates (e g. methoxymethylcarbonate), sulfonates (e gtosylate, mesylate), acyclic ketal (e g dimethyl acetal); cyclic ketals(e.g., 1,3-dioxane or 1,3-dioxolanes); acyclic acetal; cyclic acetal,acyclic hemiacetal, cyclic hemiacetal, and cyclic dithioketals (e.g.,1,3-dithiane or 1,3-dithiolane).

“Leaving group” as used herein refers to any atom or moiety that iscapable of being displaced by another atom or moiety in a chemicalreaction. More specifically, in some embodiments, “leaving group” refersto the atom or moiety that is displaced in a nucleophilic substitutionreaction hi some embodiments, “leaving groups” are any atoms or moietiesthat are conjugate bases of strong acids Examples of suitable leavinggroups include, but are not limited to, tosylates and halogensNon-limiting characteristics and examples of leaving groups can befound, for example in Organic Chemistry, 2d ed, Francis Carey (1992),pages 328-331, Introduction to Organic Chemistry, 2d ed., AndrewStreitwieser and Clayton Heathcock (1981), pages 169-171; and OrganicChemistry, 5^(th) ed., John McMurry (2000), pages 398 and 408; all ofwhich are incorporated herein by reference for the limited purpose ofdisclosing characteristics and examples of leaving groups.

As used herein, the abbreviations for any protective groups, ammo acidsand other compounds, are, unless indicated otherwise, in accord withtheir common usage, recognized abbreviations, or the IUPAC-IUBCommission on Biochemical Nomenclature (See, Biochem. 1972 11:942-944).

A “prodrug” refers to an agent that is converted into the parent drug invivo. Prodrugs are often useful because, in some situations, they may beeasier to administer than the parent drug. They may, for instance, bebioavailable by oral administration whereas the parent is not. Theprodrug may also have improved solubility in pharmaceutical compositionsover the parent drug. Examples of prodrugs include compounds that haveone or more biologically labile groups attached to the parent drug(e.g., a compound of Formula I and/or a compound of Formula II). Forexample, one or more biologically labile groups can be attached to afunctional group of the parent drug (for example, by attaching one ormore biologically labile groups to a phosphate). When more than onebiologically labile groups is attached, the biologically labile groupscan be the same or different. The biologically labile group(s) can belinked (for example, through a covalent bond), to an oxygen or aheteroatom, such as a phosphorus of a monophosphate, diphosphate,triphosphate, and/or a stabilized phosphate analog containing carbon,nitrogen or sulfur (referred to hereinafter in the present paragraph as“phosphate”). In instances where the prodrug is form by attaching one ormore biologically labile groups to the phosphate, removal of thebiologically labile group in the host produces a phosphate. The removalof the biologically labile group(s) that forms the prodrug can beaccomplished by a variety of methods, including, but not limited to,oxidation, reduction, amination, deamination, hydroxylation,dehydroxylation, hydrolysis, dehydrolysis, alkylation, dealkylation,acylation, deacylation, phosphorylation, dephosphorylation, hydrationand/or dehydration. An example, without limitation, of a prodrug wouldbe a compound which is administered as an ester (the “prodrug”) tofacilitate transmittal across a cell membrane where water solubility isdetrimental to mobility but which then is metabolically hydrolyzed tothe carboxylic acid, the active entity, once inside the cell wherewater-solubility is beneficial. A further example of a prodrug mightcomprise a short peptide (polyaminoacid) bonded to an acid group wherethe peptide is metabolized or cleaved to reveal the active moiety.Additional examples of prodrug moieties include the following:R*,R*C(═O)OCH₂—, R*C(═O)SCH₂CH₂—, R*C(═O)SCHR′NH—, phenyl-O—, N-linkedamino acids, O-linked amino acids, peptides, carbohydrates, and lipids,wherein each R is independently selected from an alkyl, an alkenyl, analkynyl, an aryl, an aralkyl, acyl, sulfonate ester, a lipid, an—N-linked amino acid, an —O-linked amino acid, a peptide and acholesterol. The prodrug can be a carbonate. The carbonate can be acyclic carbonate. The cyclic carbonate can contain a carbonyl groupbetween two hydroxyl groups that results in the formation of a five orsix membered ring. Conventional procedures for the selection andpreparation of suitable prodrug derivatives are described, for example,in Design of Prodrugs, (ed. H. Bundgaard, Elsevier, 1985), which ishereby incorporated herein by reference for the limited purpose ofdescribing procedures and preparation of suitable prodrug derivatives.

The term “pro-drug ester” refers to derivatives of the compoundsdisclosed herein formed by the addition of any of several ester-forminggroups that are hydrolyzed under physiological conditions. Examples ofpro-drug ester groups include pivaloyloxymethyl, acetoxymethyl,phthalidyl, indanyl and methoxymethyl, as well as other such groupsknown in the art, including a (5-R-2-oxo-1,3-dioxolen-4-yl)methyl group.Other examples of pro-drug ester groups can be found in, for example, T.Higuchi and V. Stella, in “Pro-drugs as Novel Delivery Systems”, Vol.14, A.C.S. Symposium Series, American Chemical Society (1975); and“Bioreversible Carriers in Drug Design: Theory and Application”, editedby E. B. Roche, Pergamon Press: New York, 14-21 (1987) (providingexamples of esters useful as prodrugs for compounds containing carboxylgroups). Each of the above-mentioned references is herein incorporatedby reference for the limited purpose of disclosing ester-forming groupsthat can form prodrug esters.

The term “pharmaceutically acceptable salt” refers to a salt of acompound that does not cause significant irritation to an organism towhich it is administered and does not abrogate the biological activityand properties of the compound. In some embodiments, the salt is an acidaddition salt of the compound. Pharmaceutical salts can be obtained byreacting a compound with inorganic acids such as hydrohalic acid (e.g.,hydrochloric acid or hydrobromic acid), sulfuric acid, nitric acid,phosphoric acid and the like. Pharmaceutical salts can also be obtainedby reacting a compound with an organic acid such as aliphatic oraromatic carboxylic or sulfonic acids, for example acetic, succinic,lactic, malic, tartaric, citric, ascorbic, nicotinic, methanesulfonic,ethanesulfonic, p-toluensulfonic, salicylic or naphthalenesulfonic acid.Pharmaceutical salts can also be obtained by reacting a compound with abase to form a salt such as an ammonium salt, an alkali metal salt, suchas a sodium or a potassium salt, an alkaline earth metal salt, such as acalcium or a magnesium salt, a salt of organic bases such asdicyclohexylamine, N-methyl-D-glucamine, tris(hydroxymethyl)methylamine,C₁-C₇ alkylamine, cyclohexylamine, triethanolamine, ethylenediamine, andsalts with amino acids such as arginine, lysine, and the like.

The term “protected” as used herein and unless otherwise defined refersto a group that is added to an oxygen, nitrogen, or phosphorus atom toprevent its further reaction or for other purposes. A wide variety ofoxygen and nitrogen protecting groups are known to those skilled in theart of organic synthesis. The term aryl, as used herein, and unlessotherwise specified, refers to phenyl, biphenyl, or naphthyl, andpreferably phenyl. The aryl group can be optionally substituted with oneor more moieties selected from the group consisting of hydroxyl, amino,alkylamino, arylamino, alkoxy, aryloxy, nitro, cyano, sulfonic acid,sulfate, phosphonic acid, phosphate, or phosphonate, either unprotected,or protected as necessary, as known to those skilled in the art, forexample, as taught in Greene, et al., Protective Groups in OrganicSynthesis, John Wiley and Sons, Second Edition, 1991.

The term purine or pyrimidine base includes, but is not limited to,adenine, N⁶-alkylpurines, N⁶-acylpurines (wherein acyl is C(O)(alkyl,aryl, alkylaryl, or arylalkyl), N⁶-benzylpurine, N⁶-halopurine,N⁶-vinylpurine, N⁶-acetylenic purine, N⁶-acyl purine, N⁶-hydroxyalkylpurine, N⁶-thioalkyl purine, N²-alkylpurines, N²-alkyl-6-thiopurines,thymine, cytosine, 5-fluorocytosine, 5-methylcytosine, 6-azapyrimidine,including 6-azacytosine, 2- and/or 4-mercaptopyrmidine, uracil,5-halouracil, including 5-fluorouracil, C⁵-alkylpyrimidines,C⁵-benzylpyrimidines, C⁵-halopyrimidines, C⁵-vinylpyrimidine,C⁵-acetylenic pyrimidine, C⁵-acyl pyrimidine, C⁵-hydroxyalkyl purine,C⁵-amidopyrimidine, C⁵-cyanopyrimidine, C⁵-nitropyrimidine,C⁵-aminopyrimidine, N²-alkylpurines, N²-alkyl-6-thiopurines,5-azacytidinyl, 5-azauracilyl, triazolopyridinyl, imidazolopyridinyl,pyrrolopyrimidinyl, and pyrazolopyrimidinyl. Purine bases include, butare not limited to, guanine, adenine, hypoxanthine, 2,6-diaminopurine,2-chloro-2-aminopurine, inosine, and 6-chloropurine. Functional oxygenand nitrogen groups on the base can be protected as necessary ordesired. Suitable protecting groups are well known to those skilled inthe art, and include trimethylsilyl, dimethylhexylsilyl,t-butyldimethylsilyl, and t-butyldiphenylsilyl, trityl, alkyl groups,acyl groups such as acetyl and propionyl, methanesulfonyl, andp-toluenesulfonyl.

The term acyl refers to a carboxylic acid ester in which thenon-carbonyl moiety of the ester group is selected from straight,branched, or cyclic alkyl or lower alkyl, alkoxyalkyl includingmethoxymethyl, aralkyl including benzyl, aryloxyalkyl such asphenoxymethyl, aryl including phenyl optionally substituted withhalogen, C₁ to C₄ alkyl or C₁ to C₄ alkoxy, sulfonate esters such asalkyl or aralkyl sulphonyl including methanesulfonyl, the mono, di ortriphosphate ester, trityl or monomethoxytrityl, substituted benzyl,trialkylsilyl (e.g. dimethyl-t-butylsilyl) or diphenylmethylsilyl. Arylgroups in the esters optimally comprise a phenyl group. Acyl can alsoinclude a natural or synthetic amino acid moiety.

As used herein, the term “substantially free of” or “substantially inthe absence of” refers to a nucleoside composition that includes atleast 95% to 98%, or more preferably, 99% to 100%, of the designatedenantiomer of that nucleoside.

Similarly, the term “isolated” refers to a nucleoside composition thatincludes at least 85 or 90% by weight, preferably 95% to 98% by weight,and even more preferably 99% to 100% by weight, of the nucleoside, theremainder comprising other chemical species or enantiomers.

The term “host,” as used herein, refers to a unicellular ormulticellular organism in which the virus can replicate, including celllines and animals, and preferably a human. Alternatively, the host canbe carrying a part of the viral genome, whose replication or functioncan be altered by the compounds of the present invention. The term hostspecifically refers to infected cells, cells transfected with all orpart of the viral genome and animals, in particular, primates (includingchimpanzees) and humans. Relative to abnormal cellular proliferation,the term “host” refers to unicellular or multicellular organism in whichabnormal cellular proliferation can be mimicked. The term hostspecifically refers to cells that abnormally proliferate, either fromnatural or unnatural causes (for example, from genetic mutation orgenetic engineering, respectively), and animals, in particular, primates(including chimpanzees) and humans. In most animal applications of thepresent invention, the host is a human patient. Veterinary applications,in certain indications, however, are clearly anticipated by the presentinvention (such as bovine viral diarrhea virus in cattle, hog choleravirus in pigs, and border disease virus in sheep).

The term “halo”, as used herein, unless otherwise indicated, includesfluoro, chloro, bromo or iodo.

The compounds of this invention may contain double bonds. When suchbonds are present, the compounds of the invention exist as cis and transconfigurations and as mixtures thereof.

Unless otherwise indicated, the alkyl and alkenyl groups referred toherein, as well as the alkyl moieties of other groups referred to herein(e.g., alkoxy), may be linear or branched, and they may also be cyclic(e.g., cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl or cycloheptyl)or be linear or branched and contain cyclic moieties. Unless otherwiseindicated, halogen includes fluorine, chlorine, bromine, and iodine.

(C₂-C₉)Heterocycloalkyl when used herein refers to pyrrolidinyl,tetrahydrofuranyl, dihydrofuranyl, tetrahydropyranyl, pyranyl,thiopyranyl, aziridinyl, oxiranyl, methylenedioxyl, chromenyl,isoxazolidinyl, 1,3-oxazolidin-3-yl, isothiazolidinyl,1,3-thiazolidin-3-yl, 1,2-pyrazolidin-2-yl, 1,3-pyrazolidin-1-yl,piperidinyl, thiomorpholinyl, 1,2-tetrahydrothiazin-2-yl,1,3-tetrahydrothiazin-3-yl, tetrahydrothiadiazinyl, morpholinyl,1,2-tetrahydrodiazin-2-yl, 1,3-tetrahydrodiazin-1-yl,tetrahydroazepinyl, piperazinyl, chromanyl, etc. One of ordinary skillin the art will understand that the connection of said (C₂-C₉)heterocycloalkyl rings is through a carbon or a sp³ hybridized nitrogenheteroatom.

(C₂-C₉)Heteroaryl when used herein refers to furyl, thienyl, thiazolyl,pyrazolyl, isothiazolyl, oxazolyl, isoxazolyl, pyrrolyl, triazolyl,tetrazolyl, imidazolyl, 1,3,5-oxadiazolyl, 1,2,4-oxadiazolyl,1,2,3-oxadiazolyl, 1,3,5-thiadiazolyl, 1,2,3-thiadiazolyl,1,2,4-thiadiazolyl, pyridyl, pyrimidyl, pyrazinyl, pyridazinyl,1,2,4-triazinyl, 1,2,3-triazinyl, 1,3,5-triazinyl,pyrazolo[3,4-b]pyridinyl, cinnolinyl, pteridinyl, purinyl,6,7-dihydro-5H-[1]pyrindinyl, benzo[b]thiophenyl,5,6,7,8-tetrahydro-quinolin-3-yl, benzoxazolyl, benzothiazolyl,benzisothiazolyl, benzisoxazolyl, benzimidazolyl, thianaphthenyl,isothianaphthenyl, benzofuranyl, isobenzofuranyl, isoindolyl, indolyl,indolizinyl, indazolyl, isoquinolyl, quinolyl, phthalazinyl,quinoxalinyl, quinazolinyl, benzoxazinyl; etc. One of ordinary skill inthe art will understand that the connection of said(C₂-C₉)heterocycloalkyl rings is through a carbon atom or a sp³hybridized nitrogen heteroatom.

(C₆-C₁₀)aryl when used herein refers to phenyl or naphthyl.

As used herein, the term antiviral nucleoside agent refers to antiviralnucleosides that have anti-HIV activity. The agents can be activeagainst other viral infections as well, so long as they are activeagainst HIV.

The term “antiviral thymidine nucleosides” refers to thymidine analogueswith anti-HIV activity, including but not limited to, AZT (zidovudine)and D4T (2′,3′-didehydro-3′deoxythymidine (stravudine), and1-□-D-Dioxolane)thymine (DOT) or their prodrugs.

The term “antiviral guanine nucleosides” refers to guanine analogueswith anti-HIV activity, including but not limited to, HBG[9-(4-hydroxybutyl)guanine], lobucavir ([1R(1alpha,2beta,3alpha)]-9-[2,3-bis(hydroxymethyl)cyclobutyl]guanine),abacavir((1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]-2-cyclopentene-1-methanolsulfate (salt), a prodrug of a G-carbocyclic nucleoside) and additionalantiviral guanine nucleosides disclosed in U.S. Pat. No. 5,994,321

The term “antiviral cytosine nucleosides” refers to cytosine analogueswith anti-HIV activity, including but not limited to,(−)-2′,3′-dideoxy-3′-thiacytidine (3TC) and its 5-fluoro analog[(−)-FTC, Emtricitabine], 2′,3′-dideoxycytidine (DDC), Racivir,beta-D-2′,3′-didehydro-2′,3′-dideoxy-5-fluorocytidine (DFC, D-d4FC, RVT,Dexelvucitabine) and its enantiomer L-D4FC, and apricitabine (APC,AVX754, BCH-10618).

The term “antiviral adenine nucleosides” refers to adenine analogueswith anti-HIV activity, including, but not limited to2′,3′-dideoxy-adenosine (ddAdo), 2′,3′-dideoxyino sine (DDI),9-(2-phosphonylmethoxyethyl)adenine (PMEA), 9-R-2-phosphonomethoxypropyladenine (PMPA, Tenofovir) (K65R is resistant to PMPA), Tenofovirdisoproxil fumarate(9-[(R)-2[[bis[[isopropoxycarbonyl)oxy]-methoxy]-phosphinyl]methoxy]propyl]adeninefumarate, TDF), bis(isopropyloxymethylcarbonyl)PMPA [bis(poc)PMPA],GS-9148 (Gilead Sciences) as well as those disclosed in Balzarini, J.;De Clercq, E. Acyclic purine nucleoside phosphonates as retrovirusinhibitors. In: Jeffries D J, De Clercq E., editors. Antiviralchemotherapy. New York, N.Y.: John Wiley & Sons, Inc.; 1995. pp. 41-45,the contents of which are hereby incorporated by reference.

The term AZT is used interchangeably with the term zidovudinethroughout. Similarly, abbreviated and common names for other antiviralagents are used interchangeably throughout.

As used herein, the term DAPD ((2R,4R)-2-amino-9-[(2-hydroxymethyl)-I,3-dioxolan-4-yl]adenine) is also intended to include a related form ofDAPD known as APD [(−)-β-D-2-aminopurine dioxolane], as well as alloptically active forms of DAPD, including optically active forms andracemic forms and its phosphate prodrugs as well as dioxolane-G and the6-methoxy or 6-chloro derivatives.

As used herein, the term “pharmaceutically acceptable salts” refers topharmaceutically acceptable salts which, upon administration to therecipient, are capable of providing directly or indirectly, a nucleosideantiviral agent, or that exhibit activity themselves.

As used herein, the term “prodrug,” in connection with nucleosideantiviral agents, refers to the 5′ and N-acylated, alkylated, orphosphorylated (including mono, di, and triphosphate esters as well asstabilized phosphates and phospholipid) derivatives of nucleosideantiviral agents. In one embodiment, the acyl group is a carboxylic acidester in which the non-carbonyl moiety of the ester group is selectedfrom straight, branched, or cyclic alkyl, alkoxyalkyl includingmethoxymethyl, aralkyl including benzyl, aryloxyalkyl includingphenoxymethyl, aryl including phenyl optionally substituted by halogen,alkyl, alkyl or alkoxy, sulfonate esters such as alkyl or aralkylsulphonyl including methanesulfonyl, trityl or monomethoxytrityl,substituted benzyl, trialkylsilyl, or diphenylmethylsilyl. Aryl groupsin the esters optimally comprise a phenyl group. The alkyl group can bestraight, branched or cyclic and is preferably C₁₋₁₈.

As used herein, the term “resistant virus” refers to a virus thatexhibits a three, and more typically, five or greater fold increase inEC₅₀ compared to naive virus in a constant cell line, including, but notlimited to peripheral blood mononuclear (PBM) cells, or MT2 or MT4cells.

As used herein, the term “substantially pure” or “substantially in theform of one optical isomer” refers to a composition that includes atleast 95% to 98%, or more, preferably 99% to 100%, of a singleenantiomer of the JAK inhibitors described herein, and, optionally, tosimilar concentrations of a single enantiomer of a nucleoside. In apreferred embodiment, the JAK inhibitors are administered insubstantially pure form.

I. TREM-1 Inhibitors

TREM-1 is a triggering receptor expressed in myeloid cells. TREM-1inhibitors may be any compound, chemical, antibody, or peptide,naturally occurring or synthetic, that directly or indirectly decreasesthe activity of TREM-1. Functionally conservative variations of knownTREM-1 inhibitors are also intended to be covered by this description.This includes, for example only, deuterated variations of knowninhibitors, inhibitors comprising non-naturally occurring amino-acids,functional variations of peptide inhibitors involving a differentsequence of amino acids, inhibitors created by codon variations whichcode for the same amino-acid sequence of a known inhibitor or functionalvariation thereof, versions of peptides described herein in which one ormore of the amino acids can be, individually, D or L isomers. Theinvention also includes combinations of L-isoforms with D-isoforms.

Common TREM-1 inhibitors include peptides which may be derived fromTREM-1, or TREM-like-transcript-1 (“TLT-1”). Any peptide whichcompetitively binds TREM-1 ligands, thereby reducing TREM-1 expressionis a TREM-1 inhibitor. These peptides may be referred to as “decoyreceptors.”

Patent application EP 2555789A1 discloses peptides that inhibit TREM-1activity. Examples of such peptides are listed below in Table 1:

TABLE 1 Polypeptide Name Sequence Sequence ID TLT-1-CDR2 SAVDRRAPAGRRSEQ ID NO 1 TLT-1-CDR3 CMVDGARGPQILHR SEQ ID NO 2 LR17 LQEEDAGEYGCMVDGARSEQ ID NO 3 LR6-1 LQEEDA SEQ ID NO 4 LR6-2 EDAGEY SEQ ID NO 5 LR6-3GEYGCM SEQ ID NO 6 LR12 LQEEDAGEYGCM SEQ ID NO 7

LR17 is a known, naturally occurring direct inhibitor of TREM-1 whichfunctions by binding and trapping TREM-1 ligand. LR12 is a 12 amino-acidpeptide derived from LR17. LR12 is composed of the N-terminal 12amino-acids from LR17. Research suggests that LR12 is an equivalentTREM-1 inhibitor when compared to LR17.

The F-c portion of human IgG (AdTREM-1Ig) is a soluble inhibitor ofTREM-1 function.

LR6-1, LR6-2 and LR6-3 are all 6 amino-acids peptides derived from LR17.These peptides are known to protect mice against polymicrobrias sepsisand may function in the same manner as LR12. Patent application WO 2014037565 A2 discloses additional peptides derived from TREM-1 and TLT-1which are known to directly inhibit TREM-1 and decrease TREM-1associated inflammatory responses.

Additional examples of TREM-1 inhibitors include those disclosed bypatent application WO 2015 018936 A1. These include, but are not limitedto, antibodies directed to TREM-1 and/or sTREM-1 or TREM-1 and/orsTREM-1 ligand, small molecules inhibiting the function, activity orexpression of TREM-1, peptides inhibiting the function, activity orexpression of TREM-1, siRNAs directed to TREM-1, shRNAs directed toTREM-1, antisense oligonucleotide directed to TREM-1, ribozymes directedto TREM-1 and aptamers which bind to and inhibit TREM-1.

PCT WO 2011 047097 A2 discloses inhibition of TREM-1 by variant peptidesbiding to the transmembrane region of the DAP-12 subunit. As describedin the published, but later abandoned U.S. patent publications20090081199 and 20030165875, fusion proteins between human IgG1 constantregion and the extracellular domain of mouse TREM-1 or that of humanTREM-1 can be used, as a decoy receptor, to inhibit TREM-1. These, andall other, TREM-1 and TLT-1 derived peptides can be stabilized bymicelles to increase their effectiveness.

Another TREM-1 inhibitor is TLT-1, as disclosed in Washington, et al.,“A TREM family member, TLT-1, is found exclusively in the alpha-granulesof megakaryocytes and platelets,” Blood. 2004 Aug. 15; 104(4):1042-7.

Additional TREM-1 inhibitors include MicroRNA 294, which has been shownto target TREM-1 by dual-luciferase assay activity.

Additionally, the signaling chain homo-oligomerization (SCHOOL) model ofimmune signaling can be used to design ligand-independent peptide-basedTREM-1 inhibitors.

Naturally-occurring TREM-1 inhibitors include curcumin anddiferuloylmethane, a yellow pigment present in turmeric. Inhibition ofTREM-1 by curcumin is oxidant independent. Accordingly, curcumin andsynthetic curcumin analogs, such as those described in U.S. PublicationNos. 20150087937, 20150072984, 20150011494, 20130190256; 20130156705,20130296527, 20130224229, 20110229555; and 20030153512; U.S. Pat. Nos.7,947,687, 8,609,723, and PCT WO 2003105751.

In peripheral blood mononuclear cells, human cathelicidin LL-37suppresses synergistic responses to TREM-1 and TLR4 stimulation, partlythrough the inhibition of TREM-1 expression on monocytes.

Treatment of cells with NF-kappaB inhibitors has been shown to abolishthe expression of message of TREM-1 induced by LPS and P. aeruginosa. Incontrast, the expression of TREM-1 was increased after stimulation withLPS or P. aeruginosa in cells that had gene of PU. 1 silenced.Additionally, over-expression of PU. 1 led to inhibition of TREM-1induction in response to LPS and P. aeruginosa. These data suggest thatboth these transcription factors are involved in the expression ofTREM-1. NF-kappaB functions as a positive regulator whereas PU. 1 is anegative regulator of the TREM-1 gene.

Antibodies have been shown to inhibit TREM-1 as well. Representativeantibodies are described, for example, in U.S. Publication No.20130309239 and U.S. Pat. No. 9,000,127.

Each of the peptides described herein can be delivered usingnanoparticles.

Each of the peptides described herein can optionally be deuterated atone or more positions.

Each of the peptides described herein can optionally include D-aminoacids, and/or tails, such as polylysine tails, to stabilize thepeptides. These tails are typically at the C-terminal end of thepeptide. The C-terminal modifications can include retention signals,while the N-terminal end can include targeting signals. Common retentionsignals include the amino acid sequences -KDEL (Lys-Asp-Glu-Leu) and-HDEL (His-Asp-Glu-Leu) at the C-terminus. These tails keep the proteinin the endoplasmic reticulum and prevent it from entering the secretorypathway.

Other C-terminal modifications include post-translational modifications,most commonly by adding a lipid anchor to the C-terminus. The lipidanchor allows the protein to be inserted into a membrane without havinga transmembrane domain.

Another form of C-terminal modification is prenylation. Duringprenylation, a farnesyl- or geranylgeranyl-isoprenoid membrane anchor isadded to a cysteine residue near the C-terminus. Small, membrane-bound Gproteins are often modified this way.

Another form of C-terminal modification is the addition of aphosphoglycan, glycosylphosphatidylinositol (GPI), as a membrane anchor.The GPI anchor is attached to the C-terminus after proteolytic cleavageof a C-terminal propeptide.

II. JAK Inhibitors

In one embodiment, the TREM-1 inhibitors are administered in combinationor alternation with JAK inhibitors. Representative JAK inhibitorsinclude those disclosed in U.S. Pat. No. 7,598,257, an example of whichis Ruxolitinib (Jakafi, Incyte), which has the structure shown below:

Representative JAK inhibitors also include those disclosed in U.S. Pat.Nos. Re 41,783; 7,842,699; 7,803,805; 7,687,507; 7,601,727; 7,569,569;7,192,963; 7,091,208; 6,890,929, 6,696,567; 6,962,993; 6,635,762;6,627,754; and 6,610,847, an example of which is Tofacitinib, which hasthe structure shown below:

Tofacitinib (Pfizer), and which has the chemical name 3-{(3R,4R)-4methyl-3-[methyl-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-amino]-piperidin-1-yl}-3-oxo-propionitrile.

In one embodiment, the compounds have the formula:

wherein:

or the pharmaceutically acceptable salt or prodrug thereof; wherein

R¹ is a group of the formula

wherein y is 0, 1 or 2;

R⁴ is selected from the group consisting of hydrogen, (C₁-C₆)alkyl,(C₁-C₆)alkylsulfonyl, (C₂-C₆)alkenyl, (C₂-C₆)alkynyl wherein the alkyl,alkenyl and alkynyl groups are optionally substituted by deuterium,hydroxy, amino, trifluoromethyl, (C₁-C₄)alkoxy, (C₁-C₆)acyloxy,(C₁-C₆)alkylamino, ((C₁-C₆)alkyl)₂amino, cyano, nitro, (C₂-C₆)alkenyl,(C₂-C₆)alkynyl or (C₁-C₆)acylamino; or

R⁴ is (C₃-C₁₀)cycloalkyl wherein the cycloalkyl group is optionallysubstituted by deuterium, hydroxy, amino, trifluoromethyl,(C₁-C₆)acyloxy, (C₁-C₆)acylamino, (C₁-C₆)alkylamino,((C₁-C₆)alkyl)₂amino, cyano, cyano(C₁-C₆)alkyl,trifluoromethyl(C₁-C₆)alkyl, nitro, nitro(C₁-C₆)alkyl or(C₁-C₆)acylamino;

R⁵ is (C₂-C₉)heterocycloalkyl wherein the heterocycloalkyl groups mustbe substituted by one to five carboxy, cyano, amino, deuterium, hydroxy,(C₁-C₆)alkyl, (C₁-C₆)alkoxy, halo, (C₁-C₆)acyl, (C₁-C₆)alkylamino,amino(C₁-C₆)alkyl, (C₁-C₆)alkoxy-CO—NH, (C₁-C₆)alkylamino-CO—,(C₂-C₆)alkenyl, (C₂-C₆) alkynyl, (C₁-C₆)alkylamino, amino(C₁-C₆)alkyl,hydroxy(C₁-C₆)alkyl, (C₁-C₆)alkoxy(C₁-C₆)alkyl,(C₁-C₆)acyloxy(C₁-C₆)alkyl, nitro, cyano(C₁-C₆)alkyl, halo(C₁-C₆)alkyl,nitro(C₁-C₆)alkyl, trifluoromethyl, trifluoromethyl(C₁-C₆)alkyl,(C₁-C₆)acylamino, (C₁-C₆)acylamino(C₁-C₆)alkyl,(C₁-C₆)alkoxy(C₁-C₆)acylamino, amino(C₁-C₆)acyl,amino(C₁-C₆)acyl(C₁-C₆)alkyl, (C₁-C₆)alkylamino(C₁-C₆)acyl,((C₁-C₆)alkyl)₂amino(C₁-C₆)acyl, R¹⁵R¹⁶N—CO—O—, R¹⁵R¹⁶N—CO—(C₁-C₆)alkyl,(C₁-C₆)alkyl-S(O)_(m), R¹⁵R¹⁶NS(O)_(m), R¹⁵R¹⁶NS(O)_(m)(C₁-C₆)alkyl,R¹⁵S(O)_(m)R¹⁶N, R¹⁵S(O)_(m)R¹⁶(C₁-C₆)alkyl wherein m is 0, 1 or 2 andR¹⁵ and R¹⁶ are each independently selected from hydrogen or(C₁-C₆)alkyl; or a group of the formula

wherein a is 0, 1, 2, 3 or 4;

b, c, e, f and g are each independently 0 or 1;

d is 0, 1, 2, or 3;

X is S(O)_(n) wherein n is 0, 1 or 2; oxygen, carbonyl or —C(═N-cyano)-;

Y is S(O)_(n) wherein n is 0, 1 or 2; or carbonyl; and

Z is carbonyl, C(O)O—, C(O)NR— or S(O)_(n) wherein n is 0, 1 or 2;

R⁶, R⁷, R⁸, R⁹, R¹⁰ and R¹¹ are each independently selected from thegroup consisting of hydrogen or (C₁-C₆)alkyl optionally substituted bydeuterium, hydroxy, amino, trifluoromethyl, (C₁-C₆)acyloxy,(C₁-C₆)acylamino, (C₁-C₆)alkylamino, ((C₁-C₆)alkyl)₂amino, cyano,cyano(C₁-C₆)alkyl, trifluoromethyl(C₁-C₆)alkyl, nitro, nitro(C₁-C₆)alkylor (C₁-C₆)acylamino;

R¹² is carboxy, cyano, amino, oxo, deuterium, hydroxy, trifluoromethyl,(C₁-C₆)alkyl, trifluoromethyl(C₁-C₆)alkyl, (C₁-C₆)alkoxy, halo,(C₁-C₆)acyl, (C₁-C₆)alkylamino, ((C₁-C₆)alkyl)₂amino, amino(C₁-C₆)alkyl,(C₁-C₆)alkoxy-CO—NH, (C₁-C₆)alkylamino-CO—, (C₂-C₆)alkenyl, (C₂-C₆)alkynyl, (C₁-C₆)alkylamino, hydroxy(C₁-C₆)alkyl,(C₁-C₆)alkoxy(C₁-C₆)alkyl, (C₁-C₆)acyloxy(C₁-C₆)alkyl, nitro,cyano(C₁-C₆)alkyl, halo(C₁-C₆)alkyl, nitro(C₁-C₆)alkyl, trifluoromethyl,trifluoromethyl(C₁-C₆)alkyl, (C₁-C₆)acylamino,(C₁-C₆)acylamino(C₁-C₆)alkyl, (C₁-C₆)alkoxy(C₁-C₆)acylamino,amino(C₁-C₆)acyl, amino(C₁-C₆)acyl(C₁-C₆)alkyl,(C₁-C₆)alkylamino(C₁-C₆)acyl, ((C₁-C₆)alkyl)₂amino(C₁-C₆)acyl,R¹⁵R¹⁶N—CO—O—, R¹⁵R¹⁶N—CO—(C₁-C₆)alkyl, R¹⁵C(O)NH, R¹⁵C(O)NH,R¹⁵NHC(O)NH, (C₁-C₆)alkyl-S(O)_(m), (C₁-C₆)alkyl-S(O)_(m)—(C₁-C₆)alkyl,R¹⁵R¹⁶NS(O)_(m), R¹⁵R¹⁶NS(O)_(m)(C₁-C₆)alkyl, R¹⁵S(O)_(m)R¹⁶N,R¹⁵S(O)_(m)R¹⁶N(C₁-C₆)alkyl wherein m is 0, 1 or 2 and R¹⁵ and R¹⁶ areeach independently selected from hydrogen or (C₁-C₆)alkyl;

R² and R³ are each independently selected from the group consisting ofhydrogen, deuterium, amino, halo, hydroxy, nitro, carboxy,(C₂-C₆)alkenyl, (C₂-C₆)alkynyl, trifluoromethyl, trifluoromethoxy,(C₁-C₆)alkyl, (C₁-C₆)alkoxy, (C₃-C₁₀)cycloalkyl wherein the alkyl,alkoxy or cycloalkyl groups are optionally substituted by one to threegroups selected from halo, hydroxy, carboxy, amino (C₁-C₆)alkylthio,(C₁-C₆)alkylamino, ((C₁-C₆)alkyl)₂amino, (C₅-C₉)heteroaryl,(C₂-C₉)heterocycloalkyl, (C₃-C₉)cycloalkyl or (C₆-C₁₀)aryl; or R² and R³are each independently (C₃-C₁₀)cycloalkyl, (C₃-C₁₀)cycloalkoxy,(C₁-C₆)alkylamino, ((C₁-C₆)alkyl)₂amino, (C₆-C₁₀)arylamino,(C₁-C₆)alkylthio, (C₆-C₁₀)arylthio, (C₁-C₆)alkylsulfinyl,(C₆-C₁₀)arylsulfinyl, (C₁-C₆)alkylsulfonyl, (C₆-C₁₀)arylsulfonyl,(C₁-C₆)acyl, (C₁-C₆)alkoxy-CO—NH—, (C₁-C₆)alkylamino-CO—,(C₅-C₉)heteroaryl, (C₂-C₉)heterocycloalkyl or (C₆-C₁₀)aryl wherein theheteroaryl, heterocycloalkyl and aryl groups are optionally substitutedby one to three halo, (C₁-C₆)alkyl, (C₁-C₆)alkyl-CO—NH—,(C₁-C₆)alkoxy-CO—NH—, (C₁-C₆)alkyl-CO—NH—(C₁-C₆)alkyl,(C₁-C₆)alkoxy-CO—NH—(C₁-C₆)alkyl, (C₁-C₆)alkoxy-CO—NH—(C₁-C₆)alkoxy,carboxy, carboxy(C₁-C₆)alkyl, carboxy(C₁-C₆)alkoxy,benzyloxycarbonyl(C₁-C₆)alkoxy, (C₁-C₆)alkoxycarbonyl(C₁-C₆)alkoxy,(C₆-C₁₀)aryl, amino, amino(C₁-C₆)alkyl, (C₁-C₆)alkoxycarbonylamino,(C₆-C₁₀)aryl(C₁-C₆)alkoxycarbonylamino, (C₁-C₆)alkylamino,((C₁-C₆)alkyl)₂amino, (C₁-C₆)alkylamino(C₁-C₆)alkyl,((C₁-C₆)alkyl)₂amino(C₁-C₆)alkyl, hydroxy, (C₁-C₆)alkoxy, carboxy,carboxy(C₁-C₆)alkyl, (C₁-C₆)alkoxycarbonyl,(C₁-C₆)alkoxycarbonyl(C₁-C₆)alkyl, (C₁-C₆)alkoxy-CO—NH—,(C₁-C₆)alkyl-CO—NH—, cyano, (C₅-C₉)heterocycloalkyl, amino-CO—NH—,(C₁-C₆)alkylamino-CO—NH—, ((C₁-C₆)alkyl)₂amino-CO—NH—,(C₆-C₁₀)arylamino-CO—NH—, (C₅-C₉)heteroarylamino-CO—NH—,(C₁-C₆)alkylamino-CO—NH—(C₁-C₆)alkyl,((C₁-C₆)alkyl)₂amino-CO—NH—(C₁-C₆)alkyl,(C₆-C₁₀)arylamino-CO—NH—(C₁-C₆)alkyl,(C₅-C₉)heteroarylamino-CO—NH—(C₁-C₆)alkyl, (C₁-C₆)alkylsulfonyl,(C₁-C₆)alkylsulfonylamino, (C₁-C₆)alkylsulfonylamino(C₁-C₆)alkyl,(C₆-C₁₀)arylsulfonyl, (C₆-C₁₀)arylsulfonylamino,(C₆-C₁₀)arylsulfonylamino(C i-C₆)alkyl, (C₁-C₆)alkylsulfonylamino,(C₁-C₆)alkylsulfonylamino(C₁-C₆)alkyl, (C₅-C₉)heteroaryl or(C₂-C₉)heterocycloalkyl.

The JAK inhibitors also include compounds of Formula B:

including pharmaceutically acceptable salt forms or prodrugs thereof,wherein:

A¹ and A² are independently selected from C and N;

T, U, and V are independently selected from O, S, N, CR⁵, and NR⁶;

wherein the 5-membered ring formed by A¹, A², U, T, and V is aromatic;

X is N or CR⁴;

Y is C₁₋₈ alkylene, C₂₋₈ alkenylene, C₂₋₈ alkynylene,(CR¹¹R¹²)_(p)—(C₃₋₁₀ cycloalkylene)-(CR¹¹R¹²)_(q),(CR¹¹R¹²)_(p)-(arylene)-(CR¹¹R¹²)_(q), (CR¹¹R¹²)_(p)—(C₁₋₁₀heterocycloalkylene)-(CR¹¹R¹²)_(q),(CR¹¹R¹²)_(p)-(heteroarylene)-(CR¹¹R¹²)_(q),(CR¹¹R¹²)_(p)O(CR¹¹R¹²)_(q), (CR¹¹R¹²)_(p)S(CR¹¹R¹²)_(q),(CR¹¹R¹²)_(p)C(O)(CR¹¹R¹²)_(q), (CR¹¹R¹²)_(p)C(O)NR_(c)(CR¹¹R¹²)_(q),(CR¹¹R¹²)_(p)C(O)O(CR¹¹R¹²)_(q), (CR¹¹R¹²)OC(O)(CR¹¹R¹²)_(q),(CR¹¹R¹²)_(p)OC(O)NR_(c)(CR¹¹R¹²)_(q), (CR¹¹R¹²)_(p)NR_(c)(CR¹¹R¹²)_(q),(CR¹¹R¹²)_(p)NR_(c)C(O)NR_(d)(CR¹¹R¹²)_(q),(CR¹¹R¹²)_(p)S(O)(CR¹¹R¹²)_(q), (CR¹¹R¹²)_(p)S(O)NR_(c)(CR¹¹R¹²)_(q),(CR¹¹R¹²)_(p)S(O)₂(CR¹¹R¹²)_(q), or(CR¹¹R¹²)_(p)S(O)₂NR^(c)(CR¹¹R¹²)_(q), wherein said C₁₋₈ alkylene, C₂₋₈alkenylene, C₂₋₈ alkynylene, cycloalkylene, arylene,heterocycloalkylene, or heteroarylene, is optionally substituted with 1,2, or 3 substituents independently selected from -D¹-D²-D³-D⁴;

Z is H, halo, C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ haloalkyl,halosulfanyl, C₁₋₄ hydroxyalkyl, C₁₋₄ cyanoalkyl, ═C—R^(i), ═N—R^(i),Cy¹, CN, NO₂, OR^(a), SR^(a), C(O)R^(b), C(O)NR^(c)R^(d), C(O)OR^(a),OC(O)R^(b), OC(O)NR^(c)R^(d), NR^(c)R^(d),NR^(c)C(O)R^(b)NR^(c)C(O)NR^(c)R^(d), NR^(c)C(O)OR^(a),C(═NR^(i))NR^(c)R^(d), NR^(c)C(═NR^(i))NR^(c)R^(d), S(O)R^(b),S(O)NR^(c)R^(d), S(O)₂R^(b), NR^(c)S(O)₂R^(b), C(═NOH)R^(b),C(═NO(C₁₋₆alkyl)R^(b), and S(O)₂NR^(c)R^(d), wherein said C₁₋₈ alkyl,C₂₋₈ alkenyl, or C₂₋₈ alkynyl, is optionally substituted with 1, 2, 3,4, 5, or 6 substituents independently selected from halo, C₁₋₄ alkyl,C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ haloalkyl, halosulfanyl, C₁₋₄hydroxyalkyl, C₁₋₄ cyanoalkyl, Cy¹, CN, N₂, OR^(a), SR^(a), C(O)R^(b),C(O)NR^(c)R^(d), C(O)OR^(a), OC(O)R^(b)OC(O)NR^(c)R^(d), NR^(c)R^(d),NR^(c)C(O)R^(b), NR^(c)C(O)NR^(c)R^(d), NR^(c)C(O)OR^(a),C(═NR^(i))NR^(c)R^(d), NR^(c)C(═NR^(i))NR^(c)R^(d), S(O)R^(b),S(O)NR^(c)R^(d), S(O)₂R^(b), NR^(c)S(O)₂R^(b), C(═NOH)R^(b), C(═NO(C₁₋₆alkyl))R^(b), and S(O)₂NR^(c)R^(d);

wherein when Z is H, n is 1;

or the —(Y)_(n)—Z moiety is taken together with i) A² to which themoiety is attached, ii) R⁵ or R⁶ of either T or V, and iii) the C or Natom to which the R⁵ or R⁶ of either T or V is attached to form a 4- to20-membered aryl, cycloalkyl, heteroaryl, or heterocycloalkyl ring fusedto the 5-membered ring formed by A¹ A², U, T, and V, wherein said 4- to20-membered aryl, cycloalkyl, heteroaryl, or heterocycloalkyl ring isoptionally substituted by 1, 2, 3, 4, or 5 substituents independentlyselected from -(W)_(m)-Q;

W is C₁₋₈ alkylenyl, C₂₋₈ alkenylenyl, C₂₋₈ alkynylenyl, O, S, C(O),C(O)NR^(c′), C(O)O, OC(O), OC(O)NR^(c′), NR^(c′), NR^(c′)C(O)NR^(d′),S(O), S(O)NR^(c′), S(O)₂, or S(O)₂NR^(c′);

Q is H, halo, CN, NO₂, C₁₋₈ alkyl, C₂₋₈ alkenyl, C₂₋₈ alkynyl, C₁₋₈haloalkyl, halosulfanyl, aryl, cycloalkyl, heteroaryl, orheterocycloalkyl, wherein said C₁₋₈ alkyl, C₂₋₈ alkenyl, C₂₋₈ alkynyl,C₁₋₈ haloalkyl, aryl, cycloalkyl, heteroaryl, or heterocycloalkyl isoptionally substituted with 1, 2, 3 or 4 substituents independentlyselected from halo, C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄haloalkyl, halosulfanyl, C₁₋₄ hydroxyalkyl, C₁₋₄ cyanoalkyl, Cy², CN,NO₂, OR^(a′), SR^(a′), C(O)R^(b′), C(O)NR^(c)R^(d′), C(O)OR^(a′),OC(O)R^(b′), OC(O)NR^(c′)R^(d′), NR^(c′)R^(d′), NR^(c′)C(O)R^(b′),NR^(c′)C(O)N R^(c′)R^(d′), N R^(c′)C(O)OR^(a′), S(O)R^(b′), S(O)NR^(c′)R^(d′), S(O)₂R^(b′), NR^(c′)S(O)₂R^(b′), and S(O)₂N R^(c′)R^(d′);

Cy¹ and Cy² are independently selected from aryl, heteroaryl,cycloalkyl, and heterocycloalkyl, each optionally substituted by 1, 2,3, 4 or 5 substituents independently selected from halo, C₁₋₄ alkyl,C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ haloalkyl, halosulfanyl, C₁₋₄hydroxyalkyl, C₁₋₄ cyanoalkyl, CN, NO₂, OR^(a″), SR^(a″), C(O)R^(b″),C(O)NR^(c″)R^(d″), C(O)OR^(a″), OC(O)R^(b″), OC(O)N R^(c″)R^(d″),NR^(c″)R^(d″), NR^(c″)C(O)R^(b″), NR^(c″)C(O)OR^(a″), NR^(c″)S(O)R^(b″),NR^(c″)S(O)₂R^(b″), S(O)R^(b″), S(O)NR^(c″)R^(d″), S(O)₂R^(b″), andS(O)₂NR^(c″)R^(d″);

R¹, R², R³, and R⁴ are independently selected from H, halo, C₁₋₄ alkyl,C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ haloalkyl, halosulfanyl, aryl,cycloalkyl, heteroaryl, heterocycloalkyl, CN, NO₂, OR⁷, SR⁷, C(O)R⁸,C(O)NR⁹R¹0, C(O)OR⁷OC(O)R⁸, OC(O)NR⁹R¹⁰, NR⁹R¹⁰, NR⁹C(O)R⁸,NR^(c)C(O)OR⁷, S(O)R⁸, S(O)NR⁹R¹⁰, S(O)₂R⁸, NR⁹S(O)₂R⁸, and S(O)₂NR⁹R¹⁰;

R⁵ is H, halo, C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ haloalkyl,halosulfanyl, CN, NO₂, OR⁷, SR⁷, C(O)R⁸, C(O)NR⁹R¹⁰, C(O)OR⁷, OC(O)R⁸,OC(O)NR⁹R¹⁰, NR⁹R¹⁰, NR⁹C(O)R⁸, NR⁹C(O)OR⁷, S(O)R⁸, S(O)NR⁹R¹⁰, S(O)₂R⁸,NR⁹S(O)₂R⁸, or S(O)₂NR⁹R¹⁰;

R⁶ is H, C₁₋₄ alkyl, C₂₋₄ alkenyl, C₂₋₄ alkynyl, C₁₋₄ haloalkyl, OR⁷,C(O)R⁸, C(O)NR⁹R¹⁰, C(O)OR⁷, S(O)R⁸, S(O)NR⁹R¹⁰, S(O)₂R⁸, orS(O)₂NR⁹R¹⁰;

R⁷ is H, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, aryl,cycloalkyl, heteroaryl, heterocycloalkyl, arylalkyl, heteroarylalkyl,cycloalkylalkyl or heterocycloalkylalkyl;

R⁸ is H, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, aryl,cycloalkyl, heteroaryl, heterocycloalkyl, arylalkyl, heteroarylalkyl,cycloalkylalkyl or heterocycloalkylalkyl;

R⁹ and R¹⁰ are independently selected from H, C₁₋₁₀ alkyl, C₁₋₆haloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₁₋₆ alkylcarbonyl, arylcarbonyl,C₁₋₆ alkylsulfonyl, arylsulfonyl, aryl, heteroaryl, cycloalkyl,heterocycloalkyl, arylalkyl, heteroarylalkyl, cycloalkylalkyl andheterocycloalkylalkyl;

or R⁹ and R¹⁰ together with the N atom to which they are attached form a4-, 5-, 6- or 7-membered heterocycloalkyl group;

R¹¹ and R¹² are independently selected from H and -E¹-E²-E³-E⁴;

D¹ and E¹ are independently absent or independently selected from C₁₋₆alkylene, C₂₋₆ alkenylene, C₂₋₆ alkynylene, arylene, cycloalkylene,heteroarylene, and heterocycloalkylene, wherein each of the C₁₋₆alkylene, C₂₋₆ alkenylene, C₂₋₆ alkynylene, arylene, cycloalkylene,heteroarylene, and heterocycloalkylene is optionally substituted by 1, 2or 3 substituents independently selected from halo, CN, NO₂, N₃, SCN,OH, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₈ alkoxyalkyl, C₁₋₆ alkoxy, C₁₋₆haloalkoxy, amino, C₁₋₆ alkylamino, and C₂₋₈ dialkylamino;

D² and E² are independently absent or independently selected from C₁₋₆alkylene, C₂₋₆ alkenylene, C₂₋₆ alkynylene, (C₁₋₆ alkylene)_(r)-O—(C₁₋₆alkylene)_(s), (C₁₋₆ alkylene)_(r)-S—(C₁₋₆ alkylene)_(s), (C₁₋₆alkylene)_(r)-NR^(c)—(C₁₋₆ alkylene)_(s), (C₁₋₆ alkylene)_(r)-CO—(C₁₋₆alkylene)_(s), (C₁₋₆ alkylene)_(r)-COO—(C₁₋₆ alkylene)_(s), (C₁₋₆alkylene)_(r)-CONR^(c)—(C₁₋₆ alkylene)_(s), (C₁₋₆ alkylene)_(r)-SO—(C₁₋₆alkylene)_(s), (C₁₋₆ alkylene)_(r)-SO₂—(C₁₋₆ alkylene)_(s), (C₁₋₆alkylene)-SONR^(c)—(C₁₋₆ alkylene)_(s), and (C₁₋₆alkylene)_(r)-NR^(c)CONR^(f)—(C₁₋₆ alkylene)_(s), wherein each of theC₁₋₆ alkylene, C₂₋₆ alkenylene, and C₂₋₆ alkynylene is optionallysubstituted by 1, 2 or 3 substituents independently selected from halo,CN, NO₂, N₃, SCN, OH, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₈ alkoxyalkyl, C₁₋₆alkoxy, C₁₋₆ haloalkoxy, amino, C₁₋₆ alkylamino, and C₂₋₈ dialkylamino;

D³ and E³ are independently absent or independently selected from C₁₋₆alkylene, C₂₋₆ alkenylene, C₂₋₆ alkynylene, arylene, cycloalkylene,heteroarylene, and heterocycloalkylene, wherein each of the C₁₋₆alkylene, C₂₋₆ alkenylene, C₂₋₆ alkynylene, arylene, cycloalkylene,heteroarylene, and heterocycloalkylene is optionally substituted by 1, 2or 3 substituents independently selected from halo, CN, NO₂, N₃, SCN,OH, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₈ alkoxyalkyl, C₁₋₆ alkoxy, C₁₋₆haloalkoxy, amino, C₁₋₆ alkylamino, and C₂₋₈ dialkylamino;

E⁴ and E⁴ are independently selected from H, halo, C₁₋₄ alkyl, C₂₋₄alkenyl, C₂₋₄ alkynyl, C₁₋₄ haloalkyl, halosulfanyl, C₁₋₄ hydroxyalkyl,C₁₋₄ cyanoalkyl, Cy¹, CN, NO₂, OR^(a), SR^(a), C(O)R^(b),C(O)NR^(c)R^(a), C(O)OR^(a), OC(O)R^(b)OC(O)NR^(c)R^(d) NR^(c)R^(d),NR^(c)C(O)R^(b), NR^(c)C(O)NR^(c)R^(d), NR^(c)C(O)OR^(a),C(═NR^(i))NR^(c)R^(d), NR^(c)C(═NR^(i))NR^(c)R^(d), S(O)R^(b),S(O)NR^(c)R^(d), S(O)₂R^(b), NR^(c)S(O)₂R^(b), C(═NOH)R^(b), C(═NO(C₁₋₆alkyl)R^(b), and S(O)₂NR^(c)R^(d), wherein said C₁₋₈ alkyl, C₂₋₈alkenyl, or C₂₋₈ alkynyl, is optionally substituted with 1, 2, 3, 4, 5,or 6 substituents independently selected from halo, C₁₋₄ alkyl, C₂₋₄alkenyl, C₂₋₄ alkynyl, C₁₋₄ haloalkyl, halosulfanyl, C₁₋₄ hydroxyalkyl,C₁₋₄ cyanoalkyl, Cy¹, CN, NO₂, OR^(a), SR^(a), C(O)R^(b),C(O)NR^(c)R^(d), C(O)OR^(a), OC(O)R^(b)OC(O)NR^(c)R^(d), NR^(c)R^(d), NRC(O)R^(b), NR^(c)C(O)NR^(c)R^(d), NR^(c)C(O)OR^(a),C(═NR^(i))NR^(c)R^(d), NR^(c)C(═NR^(i))NR^(c)R^(d), S(O)R^(b),S(O)NR^(c)R^(d), S(O)₂R^(b), NR^(c)S(O)₂R^(b), C(═NOH)R^(b), C(═NO(C₁₋₆alkyl))R^(b), and S(O)₂NR^(C)R^(d);

R^(a) is H, Cy¹, —(C₁₋₆ alkyl)-Cy¹, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, wherein said C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₆alkenyl, or C₂₋₆ alkynyl is optionally substituted with 1, 2, or 3substituents independently selected from OH, CN, amino, halo, C₁₋₆alkyl, C₁₋₆ haloalkyl, halosulfanyl, aryl, arylalkyl, heteroaryl,heteroarylalkyl, cycloalkyl and heterocycloalkyl;

R^(b) is H, Cy¹, —(C₁₋₆ alkyl)-Cy¹, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, wherein said C₁₋₆ alkyl, C₁₋₆₁₋₆ haloalkyl, C₂₋₆alkenyl, or C₂₋₆ alkynyl is optionally substituted with 1, 2, or 3substituents independently selected from OH, CN, amino, halo, C₁₋₆alkyl, C₁₋₆ haloalkyl, C₁₋₆ haloalkyl, halosulfanyl, aryl, arylalkyl,heteroaryl, heteroarylalkyl, cycloalkyl and heterocycloalkyl;

R^(a′) and R^(a″) are independently selected from H, C₁₋₆ alkyl, C₁₋₆haloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, aryl, cycloalkyl, heteroaryl,heterocycloalkyl, arylalkyl, heteroarylalkyl, cycloalkylalkyl andheterocycloalkylalkyl, wherein said C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, aryl, cycloalkyl, heteroaryl, heterocycloalkyl,arylalkyl, heteroarylalkyl, cycloalkylalkyl or heterocycloalkylalkyl isoptionally substituted with 1, 2, or 3 substituents independentlyselected from OH, CN, amino, halo, C₁₋₆ alkyl, C₁₋₆ haloalkyl,halosulfanyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, cycloalkyland heterocycloalkyl;

R^(b′) and R^(b″) are independently selected from H, C₁₋₆ alkyl, C₁₋₆haloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, aryl, cycloalkyl, heteroaryl,heterocycloalkyl, arylalkyl, heteroarylalkyl, cycloalkylalkyl andheterocycloalkylalkyl, wherein said C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, aryl, cycloalkyl, heteroaryl, heterocycloalkyl,arylalkyl, heteroarylalkyl, cycloalkylalkyl or heterocycloalkylalkyl isoptionally substituted with 1, 2, or 3 substituents independentlyselected from OH, CN, amino, halo, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₁₋₆haloalkyl, halosulfanyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl,cycloalkyl and heterocycloalkyl;

R^(c) and R^(d) are independently selected from H, Cy¹, —(C₁₋₆alkyl)-Cy¹, C₁₋₁₀ alkyl, C₁₋₆ haloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl,wherein said C₁₋₁₀ alkyl, C₁₋₆ haloalkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynyl,is optionally substituted with 1, 2, or 3 substituents independentlyselected from Cy¹, —(C₁₋₆ alkyl)-Cy¹, OH, CN, amino, halo, C₁₋₆ alkyl,C₁₋₆ haloalkyl, C₁₋₆ haloalkyl, and halosulfanyl;

or R^(c) and R^(d) together with the N atom to which they are attachedform a 4-, 5-, 6- or 7-membered heterocycloalkyl group optionallysubstituted with 1, 2, or 3 substituents independently selected fromCy¹, —(C₁₋₆ alkyl)-Cy¹, OH, CN, amino, halo, C₁₋₆ alkyl, C₁₋₆ haloalkyl,C₁₋₆ haloalkyl, and halosulfanyl;

R^(c′) and R^(d′) are independently selected from H, C₁₋₁₀ alkyl, C₁₋₆haloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, aryl, heteroaryl, cycloalkyl,heterocycloalkyl, arylalkyl, heteroarylalkyl, cycloalkylalkyl andheterocycloalkylalkyl, wherein said C₁₋₁₀ alkyl, C₁₋₆ haloalkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, aryl, heteroaryl, cycloalkyl, heterocycloalkyl,arylalkyl, heteroarylalkyl, cycloalkylalkyl or heterocycloalkylalkyl isoptionally substituted with 1, 2, or 3 substituents independentlyselected from OH, CN, amino, halo, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₁₋₆haloalkyl, halosulfanyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl,cycloalkyl and heterocycloalkyl;

or R^(c′) and R^(d′) together with the N atom to which they are attachedform a 4-, 5-, 6- or 7-membered heterocycloalkyl group optionallysubstituted with 1, 2, or 3 substituents independently selected from OH,CN, amino, halo, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₁₋₆ haloalkyl,halosulfanyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, cycloalkyland heterocycloalkyl;

R^(c″) and R^(d″) are independently selected from H, C₁₋₁₀ alkyl, C₁₋₆haloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, aryl, heteroaryl, cycloalkyl,heterocycloalkyl, arylalkyl, heteroarylalkyl, cycloalkylalkyl andheterocycloalkylalkyl, wherein said C₁₋₁₀ alkyl, C₁₋₆ haloalkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, aryl, heteroaryl, cycloalkyl, heterocycloalkyl,arylalkyl, heteroarylalkyl, cycloalkylalkyl or heterocycloalkylalkyl isoptionally substituted with 1, 2, or 3 substituents independentlyselected from OH, CN, amino, halo, C₁₋₆ alkyl, C₁₋₆ haloalkyl,halosulfanyl, C₁₋₆ haloalkyl, aryl, arylalkyl, heteroaryl,heteroarylalkyl, cycloalkyl and heterocycloalkyl;

or R^(c″) and R^(d″) together with the N atom to which they are attachedform a 4-, 5-, 6- or 7-membered heterocycloalkyl group optionallysubstituted with 1, 2, or 3 substituents independently selected from OH,CN, amino, halo, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₁₋₆ haloalkyl,halosulfanyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, cycloalkyland heterocycloalkyl;

R^(i) is H, CN, NO₂, or C₁₋₆ alkyl;

R^(e) and R^(f) are independently selected from H and C₁₋₆ alkyl;

R^(i) is H, CN, or NO₂;

m is 0 or 1;

n is 0 or 1;

p is 0, 1, 2, 3, 4, 5, or 6;

q is 0, 1, 2, 3, 4, 5 or 6;

r is 0 or 1; and

s is 0 or 1.

Additional JAK inhibitors include CEP-701 (Lestaurtinib, CephalonTechnology), a JAK 2 FL3 kinase, AZD1480 (Astra Zeneca), a JAK 2inhibitor, LY3009104/INCB28050 (Eli Lilly, Incyte) and Baracitanib, aJAK 1/2 inhibitor, Pacritinib/SB1518 (S*BIO), a JAK 2 inhibitor, VX-509(Vertex), a JAK 3 inhibitor, GLPG0634 (Galapagos), a JAK 1 inhibitor,INC424 (Novartis), a JAK inhibitor, R-348 (Rigel), a JAK 3 inhibitor,CYT387 (YM Bioscience), a JAK1/2 inhibitor, TG 10138, a JAK 2 inhibitor,AEG 3482 (Axon), a JAK inhibitor, and pharmaceutically-acceptable saltsand prodrugs thereof.

Lestaurtinib has the following formula:

AEG 3482 has the following formula:

TG 10138 has the following formula:

CYT387 has the following formula:

AZD1480 has the following formula:

LY3009104 is believed to be(R)-3-(4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl-3-cyclopentyl-propanenitrile

Pacritinib has the following formula:

The compounds include those described in U.S. Publication Nos.20110020469; 20110118255; 20100311743; 20100310675; 20100280026;20100160287; 20100081657; 20100081645; 20090181938; 20080032963;20070259869; and 20070249031.

The compounds also include those described in U.S. Publication Nos.20110251215; 20110224157; 20110223210; 20110207754; 20110136781;20110086835; 20110086810; 20110082159; 20100190804; 20100022522;20090318405; 20090286778; 20090233903; 20090215766; 20090197869;20090181959; 20080312259; 20080312258; 20080188500; and 20080167287;20080039457.

The compounds also include those described in U.S. Publication Nos.20100311693; 20080021013; 20060128780; 20040186157; and 20030162775.

The compounds also include those described in U.S. Publication Nos.20110245256; 20100009978; 20090098137; and 20080261973.

The compounds also include those described in U.S. Publication No.20110092499. Representative compounds include:

-   7-iodo-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine-   7-(4-aminophenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine-   N-(4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)acrylamide-   7-β-aminophenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine-   N-(3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phen-yl)acrylamide-   N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine-   methyl    2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidine-7-carboxylate-   N-(4-morpholinophenyl)-5H-pyrrolo[3,2-d]pyrimidin-2-amine-   7-(4-amino-3-methoxyphenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine-   4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide-   N,N-dimethyl-3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide-   1-ethyl-3-(2-methoxy-4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)urea-   N-(4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanesulfonamide-   2-methoxy-4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenol-   2-cyano-N-(3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)acetamide-   N-(cyanomethyl)-2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidine-7-carboxamide-   N-(3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanesulfonamide-   1-ethyl-3-(4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)-2-(trifluoromethoxy)phenyl)urea-   N-(3-nitrophenyl)-7-phenylthieno[3,2-d]pyrimidin-2-amine-   7-iodo-N-(3-nitrophenyl)thieno[3,2-d]pyrimidin-2-amine-   N1-(7-(2-ethylphenyl)thieno[3,2-d]pyrimidin-2-yl)benzene-1,3-diamine-   N-tert-butyl-3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide-   N1-(7-iodothieno[3,2-d]pyrimidin-2-yl)benzene-1,3-diamine-   7-(4-amino-3-(trifluoromethoxy)phenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine-   7-(2-ethylphenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine-   N-(3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl-)acetamide-   N-(cyanomethyl)-N-(3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanesulfonamide-   N-(cyanomethyl)-N-(4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanesulfonamide-   N-(3-(5-methyl-2-(4-morpholinophenylamino)-5H-pyrrolo[3,2-d]pyrimidin-7-y-1)phenyl)methanesulfonamide-   4-(5-methyl-2-(4-morpholinophenylamino)-5H-pyrrolo[3,2-d]pyrimidin-7-yl)b-enzenesulfonamide-   N-(4-(5-methyl-2-(4-morpholinophenylamino)-5H-pyrrolo[3,2-d]pyrimidin-7-y-1)phenyl)methanesulfonamide-   7-iodo-N-(4-morpholinophenyl)-5H-pyrrolo[3,2-d]pyrimidin-2-amine-   7-(2-isopropylphenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine-   7-bromo-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine-   N7-(2-isopropylphenyl)-N2-(4-morpholinophenyl)thieno[3,2-d]pyrimidine-2,7-diamine-   N7-(4-isopropylphenyl)-N2-(4-morpholinophenyl)thieno[3,2-d]pyrimidine-2,7-diamine-   7-(5-amino-2-methylphenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine-   N-(cyanomethyl)-4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)benzamide-   7-iodo-N-(3-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine-   7-(4-amino-3-nitrophenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine-   7-(2-methoxypyridin-3-yl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine-   (3-(7-iodothieno[3,2-d]pyrimidin-2-ylamino)phenyl)methanol-   N-tert-butyl-3-(2-(3-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide-   N-tert-butyl-3-(2-(3-(hydroxymethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide-   N-(4-morpholinophenyl)-7-(4-nitrophenylthio)-5H-pyrrolo[3,2-d]pyrimidin-2-amine-   N-tert-butyl-3-(2-(3,4,5-trimethoxyphenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide-   7-(4-amino-3-nitrophenyl)-N-(3,4-dimethoxyphenyl)thieno[3,2-d]pyrimidin-2-amine-   N-(3,4-dimethoxyphenyl)-7-(2-methoxypyridin-3-yl)thieno[3,2-d]pyrimidin-2-amine-   N-tert-butyl-3-(2-(3,4-dimethoxyphenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide-   7-(2-aminopyrimidin-5-yl)-N-(3,4-dimethoxyphenyl)thieno[3,2-d]pyrimidin-2-amine-   N-(3,4-dimethoxyphenyl)-7-(2,6-dimethoxypyridin-3-yl)thieno[3,2-d]pyrimidin-2-amine-   N-(3,4-dimethoxyphenyl)-7-(2,4-dimethoxypyrimidin-5-yl)thieno[3,2-d]pyrimidin-2-amine-   7-iodo-N-(4-(morpholinomethyl)phenyl)thieno[3,2-d]pyrimidin-2-amine-   N-tert-butyl-3-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide-   2-cyano-N-(4-methyl-3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)acetamide-   ethyl    3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)benzoate-   7-bromo-N-(4-(2-(pyrrolidin-1-yl)ethoxy)phenyl)thieno[3,2-d]pyrimidin-2-amine-   N-(3-(2-(4-(2-(pyrrolidin-1-yl)ethoxy)phenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)acetamide-   N-(cyanomethyl)-3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)benzamide-   N-tert-butyl-3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)benzamide-   N-tert-butyl-3-(2-(4-(1-ethylpiperidin-4-yloxy)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide-   tert-butyl-4-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)-1H-pyrazole-1-carboxylate-   7-bromo-N-(4-((4-ethylpiperazin-1-yl)methyl)phenyl)thieno[3,2-d]pyrimidin-2-amine-   N-tert-butyl-3-(2-(4-((4-ethylpiperazin-1-yl)methyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide-   N-(4-((4-ethylpiperazin-1-yl)methyl)phenyl)-7-(1H-pyrazol-4-yl)thieno[3,2-d]pyrimidin-2-amine-   N-(cyanomethyl)-3-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzamide-   N-tert-butyl-3-(2-(4-(2-(pyrrolidin-1-yl)ethoxy)phenylamino)thieno[3,2-d]-pyrimidin-7-yl)benzenesulfonamide-   tert-butyl    pyrrolidin-1-yl)ethoxy)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzylcarb-amate-   3-(2-(4-(2-(pyrrolidin-1-yl)ethoxy)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide-   7-(3-chloro-4-fluorophenyl)-N-(4-(2-(pyrrolidin-1-yl)ethoxy)phenyl)thieno-[3,2-d]pyrimidin-2-amine-   tert-butyl    4-(2-(4-(1-ethylpiperidin-4-yloxy)phenylamino)thieno[3,2-d]pyrimidin-7-yl-)-1H-pyrazole-1-carboxylate-   7-(benzo[d][1,3]dioxol-5-yl)-N-(4-(morpholinomethyl)phenyl)thieno[3,2-d]pyrimidin-2-amine-   tert-butyl    5-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)-1H-indole-1-carboxylate-   7-(2-aminopyrimidin-5-yl)-N-(4-(morpholinomethyl)phenyl)thieno[3,2-d]pyrimidin-2-amine-   tert-butyl    4-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)-5,6-di-hydropyridine-1    (2H)-carboxylate-   tert-butyl    morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzylcarbamate-   N-(3-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)-phenyl)acetamide-   N-(4-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)acetamide-   N-(3-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanesulfonamide-   7-(4-(4-methylpiperazin-1-yl)phenyl)-N-(4-(morpholinomethyl)phenyl)thieno-[3,2-d]pyrimidin-2-amine-   N-(2-methoxy-4-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)acetamide-   7-bromo-N-(3,4,5-trimethoxyphenyl)thieno[3,2-d]pyrimidin-2-amine-   (3-(2-(3,4,5-trimethoxyphenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanol-   (4-(2-(3,4,5-trimethoxyphenylamino)thieno[3,2-d]pyrimidin-7-yl)p-henyl)methanol-   (3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanol-   (4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanol-   N-(pyrrolidin-1-yl)ethoxy)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzyl)methanesulfonamide-   tert-butyl    morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzylcarbamate-   N-(4-(morpholinomethyl)phenyl)-7-(3-(piperazin-1-yl)phenyl)thieno[3,2-d]pyrimidin-2-amine-   7-(6-(2-morpholinoethylamino)pyridin-3-yl)-N-(3,4,5-trimethoxyphenyl)thieno[3,2-d]pyrimidin-2-amine-   7-(2-ethylphenyl)-N-(4-(2-(pyrrolidin-1-yl)ethoxy)phenyl)thieno[3,2-d]pyrimidin-2-amine-   7-(4-(aminomethyl)phenyl)-N-(4-(morpholinomethyl)phenyl)thieno[3,2-d]pyrimidin-2-amine-   N-(4-(1-ethylpiperidin-4-yloxy)phenyl)-7-(1H-pyrazol-4-yl)thieno[3,2-d]pyrimidin-2-amine-   N-(2,4-dimethoxyphenyl)-7-phenylthieno[3,2-d]pyrimidin-2-amine-   7-bromo-N-(3,4-dimethoxyphenyl)thieno[3,2-d]pyrimidin-2-amine-   N-(3,4-dimethoxyphenyl)-7-phenylthieno[3,2-d]pyrimidin-2-amine-   R348 (Rigel) is defined in Velotta et al., “A novel JAK3 inhibitor,    R348, attenuates chronic airway allograft rejection,”    Transplantation. 2009 Mar. 15; 87(5):653-9.

The present invention also relates to the pharmaceutically acceptableacid addition salts of compounds of Formulas A and B, as well as theadditional JAK inhibitors described herein. The acids which are used toprepare the pharmaceutically acceptable acid addition salts of theaforementioned base compounds of this invention are those which formnon-toxic acid addition salts, i.e., salts containing pharmacologicallyacceptable anions, such as the hydrochloride, hydrobromide, hydroiodide,nitrate, sulfate, bisulfate, phosphate, acid phosphate, acetate,lactate, citrate, acid citrate, tartrate, bitartrate, succinate,maleate, fumarate, gluconate, saccharate, benzoate, methanesulfonate,ethanesulfonate, benzenesulfonate, p-toluenesulfonate and pamoate [i.e.,1,1′-methylene-bis-(2-hydroxy-3-naphthoate)] salts.

The invention also relates to base addition salts of Formulas A and B.The chemical bases that may be used as reagents to preparepharmaceutically acceptable base salts of those compounds of Formulas Aand B that are acidic in nature are those that form non-toxic base saltswith such compounds. Such non-toxic base salts include, but are notlimited to those derived from such pharmacologically acceptable cationssuch as alkali metal cations (e.g., potassium and sodium) and alkalineearth metal cations (e.g., calcium and magnesium), ammonium orwater-soluble amine addition salts such asN-methylglucamine-(meglumine), and the lower alkanolammonium and otherbase salts of pharmaceutically acceptable organic amines.

The compounds of this invention include all conformational isomers(e.g., cis and trans isomers. The compounds of the present inventionhave asymmetric centers and therefore exist in different enantiomericand diastereomeric forms. This invention relates to the use of alloptical isomers and stereoisomers of the compounds of the presentinvention, and mixtures thereof, and to all pharmaceutical compositionsand methods of treatment that may employ or contain them. In thisregard, the invention includes both the E and Z configurations. Thecompounds of Formulas A and B can also exist as tautomers. Thisinvention relates to the use of all such tautomers and mixtures thereof.

This invention also encompasses pharmaceutical compositions containingprodrugs of compounds of the Formulas A and B, and their use in treatingor preventing HIV. This invention also encompasses methods of treatingor preventing viral infections that can be treated or prevented byprotein kinase inhibitors, such as the enzyme Janus Kinase 1, 2, or 3,comprising administering prodrugs of compounds of the Formulas A and B.Compounds of Formulas A and B having free amino, amido, hydroxy orcarboxylic groups can be converted into prodrugs. Prodrugs includecompounds wherein an amino acid residue, or a polypeptide chain of twoor more (e.g., two, three or four) amino acid residues which arecovalently joined through peptide bonds to free amino, hydroxy orcarboxylic acid groups of compounds of Formulas A and B. The amino acidresidues include the 20 naturally occurring amino acids commonlydesignated by three letter symbols and also include, 4-hydroxyproline,hydroxylysine, demosine, isodemosine, 3-methylhistidine, norvlin,beta-alanine, gamma-aminobutyric acid, citrulline, homocysteine,homoserine, ornithine and methioine sulfone. Prodrugs also includecompounds wherein carbonates, carbamates, amides and alkyl esters thatare covalently bonded to the above substituents of Formulas A and Bthrough the carbonyl carbon prodrug sidechain.

IiI. Combinations of TREM-1 Inhibitors and Other Antiviral Agents

In one embodiment, the compositions include antiretroviral TREM-1inhibitors as described herein and one or more additional antiviralagents.

In one aspect of this embodiment, the TREM-1 inhibitors and additionalantiviral agents are administered in combination or alternation, and inone aspect, in a manner in which both agents act synergistically againstthe virus. The compositions and methods described herein can be used totreat patients infected with a drug resistant form of HIV, specifically,a form including the M184V/I, multidrug resistant viruses (e.g., Q151M),K65R mutation, Thymidine analog mutations (TAMS), and the like. TAMSinclude, but are not limited to, mutations at reverse transcriptase (RT)positions 41, 67, 70, 210, 215, and 219, which confer clinicallysignificant resistance to each of the nucleoside RT inhibitors with theexception of 3TC.

While not wishing to be bound to a particular theory, it is believedthat the TREM-1 inhibitors described herein function in a way notassociated with heretofore known antiretroviral therapy, in that thecompounds do not act in the same way as NRTI, NNRTI, proteaseinhibitors, integrase inhibitors, entry inhibitors, and the like, all ofwhich interfere directly with a step in the viral replication cycle.Rather, they act in an intracellular manner, in a way that is not likelyto provoke resistance. More specifically, the mechanism is independentand distinct from direct modulation or interference with the viralreplication cycle itself, and therefore lacks a selective pressure toconfer emergence of drug resistant virus.

Further, the combination of the TREM-1 inhibitors described herein, andone or more additional antiviral agents, can help prevent thedevelopment of viral resistance to other antiviral agents. Therefore,co-formulation of the TREM-1 inhibitors with these additional antiviralagents can function as a “resistance repellent” for the variousmutations associated with conventional therapy, and provides bettertherapy than either alone.

In one aspect of this embodiment, a combination therapy is administeredthat has the capability of attacking HIV in a variety of mechanisms.That is, the combination therapy includes an effective amount of atleast one adenine, cytosine, thymine, and guanosine nucleosideantiviral, as well as one or more additional agents other than NRTI thatinhibit HIV viral loads via a different mechanism. Examples includereverse transcriptase inhibitors, protease inhibitors, fusioninhibitors, entry inhibitors, attachment inhibitors, polymeraseinhibitors, and integrase inhibitors such as integrase inhibitors suchas raltegravir (Isentress) or MK-0518, GS-9137 (Gilead Sciences),GS-8374 (Gilead Sciences), or GSK-364735.

It is believed that this therapy, particularly when administered at anearly stage in the development of HIV infection, has the possibility ofeliminating HIV infection in a patient. That is, the presence of thedifferent nucleosides and additional agents minimizes the ability of thevirus to adapt its reverse transcriptase and develop resistance to anyclass of nucleoside antiviral nucleosides (i.e., adenine, cytosine,thymidine, or guanine), because it would be susceptible to at least oneof the other nucleoside antiviral agents that are present, and/or theadditional non-NRTI therapeutic agent. In addition the lipophiliccharacter of certain agents would allow them to penetrate certaincompartments where virus could replicate (e.g., brain, testicles, gut).

Representative agents are described in more detail below.

Attachment and Fusion Inhibitors

Attachment and fusion inhibitors are anti-HIV drugs which are intendedto protect cells from infection by HIV by preventing the virus fromattaching to a new cell and breaking through the cell membrane. Thesedrugs can prevent infection of a cell by either free virus (in theblood) or by contact with an infected cell. These agents are susceptibleto digestive acids, so are commonly delivered by break them down, mostof these drugs are given by injections or intravenous infusion.

Examples are shown in the table that follows:

Brand Generic Experimental Pharmaceutical Name Name Abbreviation CodeCompany Fuzeon ™ enfuvirtide T-20 Trimeris T-1249 Trimeris AMD-3100AnorMED, Inc. CD4-IgG2 PRO-542 Progenics Pharmaceuticals BMS-488043Bristol-Myers Squibb aplaviroc GSK-873,140 GlaxoSmithKline Peptide TAdvanced Immuni T, Inc. TNX-355 Tanox, Inc. maraviroc UK-427,857 PfizerCXCR4 Inhibitor AMD070 AMD11070 AnorMED, Inc. CCR5 antagonist VicrirocSCH-D SCH-417690 Schering-Plough

Additional fusion and attachment inhibitors in human trials includeAK602, AMD070, BMS-378806, HGS004, INCB9471, PRO 140, Schering C, SP01A,and TAK-652.

AK602 is a CCR5 blocker being developed by Kumamoto University in Japan.

AMD070 by AnorMed blocks the CXCR4 receptor on CD4 T-cells to inhibitHIV fusion.

BMS-378806 is an attachment inhibitor that attaches to gp120, a part ofHIV.

HGS004 by Human Genome Sciences, is a monoclonal antibody CCR5 blocker.

INCB 9471 is sold by Incyte Corporation.

PRO 140 by Progenies blocks fusion by binding to a receptor protein onthe surface of CD4 cells.

SP01A by Samaritan Pharmaceuticals is an HIV entry inhibitor.

TAK-652 by Takeda blocks binding to the CCR5 receptor.

Polymerase Inhibitors

The DNA polymerization activity of HIV-1 reverse transcriptase (RT) canbe inhibited by at least three mechanistically distinct classes ofcompounds. Two of these are chain terminating nucleoside analogs (NRTIs)and allosteric non-nucleoside RT inhibitors (NNRTIs). The third classincludes pyrophosphate mimetics such as foscarnet (phosphonoformic acid,PFA).

The reverse transcriptase has a second enzymatic activity, ribonucleaseH (RNase H) activity, which maps to a second active site in the enzyme.RNase H activity can be inhibited by various small molecules (polymeraseinhibitors). Examples include diketo acids, which bind directly to theRNase H domain, or compounds like PFA, which are believed to bind in thepolymerase domain.

Examples of these compounds are listed in the tables that follow.

HIV Therapies: Nucleoside/Nucleotide Reverse Transcriptase Inhibitors(NRTIs)

Brand Generic Experimental Pharmaceutical Name Name Abbreviation CodeCompany Dapavir, 2,6- DAPD RFS Pharma diaminopurine dioxolane Retrovir ®zidovudine AZT or ZDV GlaxoSmithKline Epivir ® lamivudine 3TCGlaxoSmithKline Combivir ® zidovudine + AZT + 3TC GlaxoSmithKlinelamivudine Trizivir ® abacavir + ABC + AZT + GlaxoSmithKlinezidovudine + 3TC lamivudine Ziagen ® abacavir ABC 1592U8 GlaxoSmithKlineEpzicom ™ abacavir + ABC + 3TC GlaxoSmithKline lamivudine Hivid ®zalcitabine ddC Hoffmann-La Roche Videx ® didanosine: ddI BMY-40900Bristol-Myers Squibb buffered versions Entecavir baraclude Bristol-MyersSquibb Videx ® EC didanosine: ddI Bristol-Myers Squibb delayed- releasecapsules Zerit ® stavudine d4T BMY-27857 Bristol-Myers Squibb Viread ™tenofovir TDF or Gilead Sciences disoproxil Bis(POC) fumarate (DF) PMPAGS-7340 Tenofovir TAF Gilead Sciences alafenamide fumarate (TAF)Emtriva ® emtricitabine (−)-FTC Gilead Sciences Truvada ® Viread + TDF +Gilead Sciences Emtriva (−)-FTC EFdA Merck 4′-ethynyl-2- fluoro-2′-deoxyadenosine Atripla ™ TDF + Gilead/BMS/Merck (−)-FTC + Sustiva ®Amdoxovir DAPD, RFS Pharma LLC AMDX Apricitabine AVX754 SPD 754 AvexaLtd Alovudine FLT MIV-310 Medivir Elvucitabine L-FD4C ACH-126443,Achillion KP-1461 SN1461, Koronis SN1212 Racivir RCV Emory UniversityDOT Emory University Dexelvucitabine Reverset D-D4FC, DFC DPC 817 EmoryUniversity GS9148 and Gilead Sciences prodrugs thereof

HIV Therapies: Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs)

Brand Generic Experimental Pharmaceutical Name Name Abbreviation CodeCompany Viramune ® nevirapine NVP BI-RG-587 Boehringer IngelheimRescriptor ® delavirdine DLV U-90152S/T Pfizer Sustiva ® efavirenz EFVDMP-266 Bristol-Myers Squibb (+)-calanolide A Sarawak Medichemcapravirine CPV AG-1549 or S-1153 Pfizer DPC-083 Bristol-Myers SquibbTMC-125 Tibotec-Virco Group TMC-278 Tibotec-Virco Group IDX12899 IdenixIDX12989 Idenix RDEA806 Ardea Bioscience, Inc. MK-4965 Merck

Integrase Inhibitors

Representative integrase inhibitors include globoidnan A, L-000870812,S/GSK1349572, S/GSK1265744, Raltegravir and Elvitegravir with or withouta pharmacokinetic (PK) booster such as ritonavir or Gilead'spharmacoenhancing agent (also referred to as a PK booster), GS 9350.

Suitable integrase inhibitors include those described in:

-   U.S. patent application Ser. No. 11/595,429, entitled “HIV INTEGRASE    INHIBITORS” filed in the name of B. Narasimhulu Naidu, et al. on    Nov. 10, 2006 and published on May 17, 2007 as U.S. Publication No.    20070111985 and assigned to Bristol-Meyers Squibb Company.-   U.S. patent application Ser. No. 11/561,039, entitled “HIV INTEGRASE    INHIBITORS” filed in the name of B. Narasimhulu Naidu, et al. on    Nov. 17, 2006 and published on Jun. 7, 2007 as U.S. Publication No.    20070129379 and assigned to Bristol-Meyers Squibb Company.-   U.S. patent application Ser. No. 11/599,580, entitled “HIV INTEGRASE    INHIBITORS” filed in the name of B. Narasimhulu Naidu, et al. on    Nov. 14, 2006 and published on May 17, 2007 as U.S. Publication No.    20070112190 and assigned to Bristol-Meyers Squibb Company.-   U.S. patent application Ser. No. 11/754,462, entitled “HIV INTEGRASE    INHIBITORS” filed in the name of B. Narasimhulu Naidu, et al. on May    29, 2007 and published on Dec. 6, 2007 as U.S. Publication No.    20070281917 and assigned to Bristol-Meyers Squibb Company.-   U.S. patent application Ser. No. 11/768,458, entitled “HIV INTEGRASE    INHIBITORS” filed in the name of Michael A. Walker, et al. on Jun.    26, 2007 and published Jan. 3, 2008 as U.S. Publication No.    20080004265 and assigned to Bristol-Meyers Squibb Company.-   U.S. patent application Ser. No. 12/132,145, entitled “HIV INTEGRASE    INHIBITORS” filed in the name of B. Narasimhulu Naidu, et al. on    Jun. 3, 2008; published on Dec. 11, 2008 as U.S. Publication No.    20080306051 and assigned to Bristol-Meyers Squibb Company.-   U.S. patent application Ser. No. 11/505,149, entitled “BICYCLIC    HETEROCYCLES AS HIV INTEGRASE INHIBITORS” filed in the name of B.    Narasimhulu Naidu, et al. on Aug. 16, 2006 and published on Dec. 7,    2006 as U.S. Publication No. 20060276466.-   U.S. patent application Ser. No. 11/590,637, entitled “HIV INTEGRASE    INHIBITORS” filed in the name of B. Narasimhulu Naidu, et al. on    Oct. 31, 2006 and published on May 17, 2007 as U.S. Publication No.    20070111984 and assigned to Bristol-Meyers Squibb Company.-   U.S. patent application Ser. No. 12/162,975, entitled “USE OF    6-(3-CHLORO-2-FLUOROBENZYL)-1-[(2S)-1-HYDROXY-3-METHYLBUTAN-2-YL]-7-METHOXY-4-OXO-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC    ACID OR SALT THEREOF FOR TREATING RETROVIRUS INFECTION” filed in the    name of Yuji Matsuzaki, et al. on Feb. 1, 2007 and published on Jan.    15, 2009 as U.S. Publication No. 20090018162.-   U.S. patent application Ser. No. 11/767,021, entitled    “6-(HETEROCYCLYL-SUBSTITUTED BENZYL)-4-OXOQUINOLINE COMPOUND AND USE    THEREOF AS HIV INTEGRASE INHIBITOR” filed in the name of Motohid,    Satoh, et al. on Jun. 22, 2007 and published on Aug. 28, 2008 as    U.S. Publication No. 20080207618.-   U.S. patent application Ser. No. 12/042,628, entitled “USE OF    QUINOLINE DERIVATIVES WITH ANTI-INTEGRASE EFFECT AND APPLICATIONS    THEREOF” filed in the name of Aurelia Mousnier, et al. on Mar. 5,    2008 and published on Jul. 3, 2008 as U.S. Publication No.    20080161350 and assigned to Bioalliance Pharma SA.-   U.S. patent application Ser. No. 12/169,367, entitled “NOVEL    PYRIMIDINECARBOXAMIDE DERIVATIVES” filed in the name of Scott L.    Harbeson on Jul. 8, 2008 and published on Feb. 5, 2009 as U.S.    Publication No. 20090035324.-   U.S. patent application Ser. No. 10/587,857, entitled “NAPHTHYRIDINE    DERIVATIVES HAVING INHIBITORY ACTIVITY AGAINST HIV INTEGRASE” filed    in the name of Teruhiko Taishi, et al. on Feb. 2, 2005 and published    on Sep. 10, 2009 as U.S. Publication No. 20090227621.-   U.S. patent application Ser. No. 11/500,387, entitled    “NITROGEN-CONTAINING HETEROARYL COMPOUNDS HAVING INHIBITORY ACTIVITY    AGAINST HIV INTEGRASE” filed in the name of Masahiro Fuji, et al. on    Aug. 8, 2006 and published on Dec. 28, 2006 as U.S. Publication No.    20060293334.-   U.S. patent application Ser. No. 12/097,859, entitled “METHODS FOR    IMPROVING THE PHARMACOKINETICS OF HIV INTEGRASE INHIBITORS” filed in    the name of Brian P. Kearney, et al. on Dec. 29, 2006 and published    on Sep. 17, 2009 as U.S. Publication No. 20090233964 and assigned to    Gilead Sciences, Inc.-   U.S. patent application Ser. No. 11/807,303, entitled “PRE-ORGANIZED    TRICYCLIC INTEGRASE INHIBITOR COMPOUNDS” filed in the name of    James M. Chen, et al. on May 25, 2007 and published on Jan. 29, 2009    as U.S. Publication No. 20090029939 and assigned to Gilead Sciences,    Inc.-   U.S. patent application Ser. No. 10/587,601, entitled “HIV INTEGRASE    INHIBITORS” filed in the name of Philip Jones, et al. on Mar. 1,    2005 and published on Jul. 12, 2007 as U.S. Publication No.    20070161639 and assigned to Merck and Co., Inc.-   U.S. patent application Ser. No. 10/592,222, entitled “HIV INTEGRASE    INHIBITORS” filed in the name of Peter D. Jones, et al. on Mar. 4,    2005 and published on Jan. 10, 2008 as U.S. Publication No.    20080009490 and assigned to Merck and Co., Inc.-   U.S. patent application Ser. No. 11/992,531, entitled “HIV INTEGRASE    INHIBITORS” filed in the name of Vincenzo Summa, et al. on Sep. 26,    2006 and published on Sep. 3, 2009 as U.S. Publication No.    20090221571 and assigned to Merck and Co., Inc.-   U.S. patent application Ser. No. 10/587,682, entitled “HIV INTEGRASE    INHIBITORS” filed in the name of Wei Han, et al. on Mar. 9, 2005 and    published on Aug. 2, 2007 as U.S. Publication No. 20070179196 and    assigned to Merck and Co., Inc.-   U.S. patent application Ser. No. 11/641,508, entitled “N-SUBSTITUTED    HYDROXYPYRIMIDINONE CARBOXAMIDE INHIBITORS OF HIV INTEGRASE” filed    in the name of Benedetta Crescenzi, et al. on Dec. 19, 2006 and    published on May 31, 2007 as U.S. Publication No. 20070123524 and    assigned to Merck and Co., Inc.-   U.S. patent application Ser. No. 11/435,671, entitled “INTEGRASE    INHIBITOR COMPOUNDS” filed in the name of Zhenhong R. Cai, et al. on    May 16, 2006 and published on Mar. 29, 2007 as U.S. Publication No.    20070072831 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 11/804,041, entitled “INTEGRASE    INHIBITORS” filed in the name of Zhenhong R. Cai, et al. on May 16,    2007 and published on Mar. 6, 2008 as U.S. Publication No.    20080058315 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 11/880,854, entitled “NOVEL HIV    REVERSE TRANSCRIPTASE INHIBITORS” filed in the name of Hongyan Guo,    et al. on Jul. 24, 2007 and published on Mar. 20, 2008 as U.S.    Publication No. 20080070920 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 10/585,504, entitled “PYRIMIDYL    PHOSPHONATE ANTIVIRAL COMPOUNDS AND METHODS OF USE” filed in the    name of Haolun Jin, et al. on Nov. 1, 2005 and published on Jun. 26,    2008 as U.S. Publication No. 20080153783 and assigned to Gilead    Sciences, Inc.-   U.S. patent application Ser. No. 11/579,772, entitled “HIV INTEGRASE    INHIBITORS” filed in the name of John S. Wai, et al. on May 3, 2005    and published on Nov. 20, 2008 as U.S. Publication No. 20080287394    and assigned to Merck and Co., Inc.-   U.S. patent application Ser. No. 10/591,914, entitled “HIV INTEGRASE    INHIBITORS” filed in the name of Matthew M. Morrissette, et al. on    Mar. 4, 2005 and published on Jun. 12, 2008 as U.S. Publication No.    20080139579 and assigned to Merck and Co., Inc.-   U.S. patent application Ser. No. 11/629,153, entitled “HIV INTEGRASE    INHIBITORS” filed in the name of John S. Wai, et al. on Jun. 3, 2005    and published on Jun. 18, 2008 as U.S. Publication No. 20080015187    and assigned to Merck and Co., Inc.-   U.S. patent application Ser. No. 12/043,636, entitled “HIV INTEGRASE    INHIBITORS, PHARMACEUTICAL COMPOSITIONS AND METHOD FOR THEIR USE”    filed in the name of Qiyue Hu, et al. on Mar. 6, 2008 and published    on Sep. 11, 2008 as U.S. Publication No. 20080221154 and assigned to    Pfizer, Inc.-   PCT WO 2007/019098, entitled “HIV INTEGRASE INHIBITORS,” listing    SmithKline Beecham Corporation, Shionogi & Co. Ltd., and Takashi    Kawasuji as applicants, and Brian Johns as an inventor, published on    Feb. 15, 2007.-   U.S. patent application Ser. No. 12/306,198, entitled “MODULATORS OF    PHARMACOKINETIC PROPERTIES OF THERAPEUTICS” filed in the name of    Desai, Manoj C., et al. and was published on Nov. 26, 2009 as U.S.    Publication No. 20090291952 and is assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 12/274,107, entitled, “INTEGRASE    INHIBITORS” filed Nov. 19, 2008 in the name of Jabri, Salman Y., et    al. and was published on Nov. 26, 2009 as U.S. Publication No.    20090291921 and is assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 12/215,605 “ANTIVIRAL COMPOUNDS”    filed on Jun. 26, 2008 in the name of Cho, Aesop, et al., and was    published on Oct. 15, 2009 as U.S. Publication No. 20090257978 and    is assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 12/097,859 METHODS FOR IMPROVING    THE PHARMACOKINETICS OF HIV INTEGRASE INHIBITORS filed on Dec. 29,    2006 in the name of Kearney; Brian P., et al. and published on Sep.    17, 2009 as U.S. Publication No. 20090233964 and assigned to Gilead    Sciences, Inc.-   U.S. patent application Ser. No. 11/658,419, entitled “PHOSPHONATE    ANALOGS OF HIV INHIBITOR COMPOUNDS” filed Jul. 26, 2005 in the name    of Boojamra; Constantine G., et al. and was published on Aug. 13,    2009 as U.S. Publication No. 20090202470 and is assigned to Gilead    Sciences, Inc.-   U.S. patent application Ser. No. 12/215,601, entitled, “ANTIVIRAL    COMPOUNDS” filed on Jun. 26, 2008 in the name of Cottell, Jeromy J.,    et al. and published on Jul. 23, 2009 as U.S. Publication No.    20090186869 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 12/217,496 entitled “MODULATORS OF    PHARMACOKINETIC PROPERTIES OF THERAPEUTICS” in the name of Desai,    Manoj C., et al. and published on Jul. 16, 2009 as U.S. Publication    No. 20090181902 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 12/340,419 entitled “INHIBITORS OF    CYTOCHROME P450” filed on Dec. 19, 2008 in the name of Desai,    Manoj C. et al. and published on Jul. 9, 2009 as U.S. Publication    No. 20090175820 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 12/195,161 entitled “COMPOSITIONS    AND METHODS FOR COMBINATION ANTIVIRAL THERAPY” filed on Aug. 20,    2008 in the name of Dahl, Terrence C. et al. and published on Jun.    4, 2009 as U.S. Publication No. 20090143314 and assigned to Gilead    Sciences, Inc.-   U.S. patent application Ser. No. 12/208,952 entitled “PROCESS AND    INTERMEDIATES FOR PREPARING INTEGRASE INHIBITORS” filed on Sep. 11,    2008 in the name of Dowdy, Eric, et al. and published on Apr. 16,    2009 as U.S. Publication No. 20090099366 and assigned to Gilead    Sciences, Inc.-   U.S. patent application Ser. No. 12/147,220 entitled “THERAPEUTIC    COMPOSITIONS AND METHODS” filed on Jun. 26, 2008 in the name of    Kearney, Brian P. et al and published on Apr. 9, 2009 as U.S.    Publication No. 20090093482 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 12/147,041 entitled “THERAPEUTIC    COMPOSITIONS AND METHODS” filed on Jun. 26, 2008 in the name of    Kearney, Brian P. et al., published on Apr. 9, 2009 as U.S.    Publication No. 20090093467 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 12/215,266 entitled “ANTIVIRAL    COMPOUNDS” filed on Jun. 26, 2008 in the name of Cai, Zhenhong R. et    al., published Feb. 19, 2009 as U.S. Publication No. 20090047252 and    assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 12/204,174 entitled “COMPOSITIONS    AND METHODS FOR COMBINATION ANTIVIRAL THERAPY” filed on Sep. 4, 2008    in the name of Dahl, Terrence C., et al., published on Feb. 5, 2009    as U.S. Publication No. 20090036408 and assigned to Gilead Sciences,    Inc.-   U.S. patent application Ser. No. 10/585,504 entitled “PYRIMIDYL    PHOSPHONATE ANTIVIRAL COMPOUNDS AND METHODS OF USE” filed on Nov. 1,    2005 in the name of Jin, Haolun et al., published on Jun. 26, 2008    as U.S. Publication No. 20080153783 and assigned to Gilead Sciences,    Inc.-   U.S. patent application Ser. No. 11/853,606 entitled “PROCESS AND    INTERMEDIATES FOR PREPARING INTEGRASE INHIBITORS” filed on Sep. 11,    2007 in the name of Dowdy, Eric, et al, published May 29, 2008 as    U.S. Publication No. 20080125594 and assigned to Gilead Sciences,    Inc.-   U.S. patent application Ser. No. 11/644,811 entitled “PROCESSES AND    INTERMEDIATES USEFUL FOR PREPARING INTEGRASE INHIBITOR COMPOUNDS”    filed on Dec. 21, 2006 in the name of Evans, Jared W. et al.,    published on Feb. 14, 2008 as U.S. Publication No. 20080039487 and    assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 10/586,627 entitled “USE OF    ADEFOVIR OR TENOFOVIR FOR INHIBITING MMTV-LIKE VIRUSES INVOLVED IN    BREAST CANCER AND PRIMARY BILIARY CIRRHOSIS” filed on Jul. 20, 2007    in the name of Cihlar, Tomas, et al., published on Dec. 6, 2007 as    U.S. Publication No. 20070281911 and assigned to Gilead Sciences,    Inc.-   U.S. patent application Ser. No. 11/435,671 entitled “INTEGRASE    INHIBITOR COMPOUNDS” filed on May 16, 2006 in the name of Cai,    Zhenhong R. et al., published on Mar. 29, 2007 as U.S. Publication    No. 20070072831 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 11/190,225 entitled “PHOSPHONATE    ANALOGS OF HIV INHIBITOR COMPOUNDS” filed on Jul. 26, 2005 in the    name of Boojamra, Constantine G. et al., published on Mar. 1, 2007    as U.S. Publication No. 20070049754 and assigned to Gilead Sciences,    Inc.-   U.S. patent application Ser. No. 10/511,182 entitled “NON NUCLEOSIDE    REVERSE TRANSCRIPTASE INHIBITORS” filed on Feb. 28, 2005 in the name    of Chen, James M. et al., published on Jun. 15, 2006 as U.S.    Publication No. 20060128692 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 11/033,422 entitled “PYRIMIDYL    PHOSPHONATE ANTIVIRAL COMPOUNDS AND METHODS OF USE” filed on Jan.    11, 2005 in the name of Jin, Haolun et al., published on Dec. 22,    2005 as U.S. Publication No. 20050282839 and assigned to Gilead    Sciences, Inc.-   U.S. patent application Ser. No. 11/040,929 entitled “METHODS OF    INHIBITION OF MMTV-LIKE VIRUSES” filed on Jan. 21, 2005 in the name    of Cihlar, Tomas et al., published on Oct. 27, 2005 as U.S.    Publication No. 20050239753 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 10/423,496 entitled “CELLULAR    ACCUMULATION OF PHOSPHONATE ANALOGS OF HIV PROTEASE INHIBITOR    COMPOUNDS” filed on Apr. 25, 2003 in the name of Arimilli, Murty N.    et al., published on Sep. 22, 2005 as U.S. Publication No.    20050209197 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 10/424,130 entitled “NON NUCLEOSIDE    REVERSE TRANSCRIPTASE INHIBITORS” filed on Apr. 25, 2003 in the name    of Chen, James M. et al., published on Sep. 8, 2005 as U.S.    Publication No. 20050197320 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 10/944,118 entitled “AZA-QUINOLINOL    PHOSPHONATE INTEGRASE INHIBITOR COMPOUNDS” filed on Sep. 17, 2004 in    the name of Jin, Haolun et al., published on Jun. 23, 2005 as U.S.    Publication No. 20050137199 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 10/903,288 entitled “NUCLEOBASE    PHOSPHONATE ANALOGS FOR ANTIVIRAL TREATMENT” filed on Jul. 30, 2004    in the name of Krawczyk, Steven H., published on Mar. 17, 2005 as    U.S. Publication No. 20050059637 and assigned to Gilead Sciences,    Inc.-   U.S. patent application Ser. No. 10/757,141 entitled “COMPOSITIONS    AND METHODS FOR COMBINATION ANTIVIRAL THERAPY” filed Jan. 13, 2004    Dahl, Terrance C. et al., published on Nov. 11, 2004 as U.S.    Publication No. 20040224917 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 10/757,122 entitled “COMPOSITIONS    AND METHODS FOR COMBINATION ANTIVIRAL THERAPY” filed on Jan. 13,    2004 Dahl, Terrance C. et al., published on Nov. 11, 2004 as U.S.    Publication No. 20040224916 and assigned to Gilead Sciences, Inc.-   U.S. patent application Ser. No. 10/687,373 entitled “PRE-ORGANIZED    TRICYCLIC INTEGRASE INHIBITOR COMPOUNDS” filed on Oct. 16, 2003 in    the name of Chen, James M. et al., published on Aug. 26, 2004 as    U.S. Publication No. 20040167124 and assigned to Gilead Sciences,    Inc.-   U.S. patent application Ser. No. 10/687,374 entitled “PRE-ORGANIZED    TRICYCLIC INTEGRASE INHIBITOR COMPOUNDS” filed on Oct. 15, 2003 in    the name of Chen, James M. et al., published on Aug. 12, 2004 as    U.S. Publication No. 20040157804 and assigned to Gilead Sciences,    Inc.-   U.S. patent application Ser. No. 10/424,186 entitled “METHOD AND    COMPOSITIONS FOR IDENTIFYING ANTI-HIV THERAPEUTIC COMPOUNDS” filed    on Apr. 25, 2003 in the name of Birkus, Gabriel et al., published on    Jun. 24, 2004 as U.S. Publication No. 20040121316 and assigned to    Gilead Sciences, Inc.-   U.S. patent application Ser. No. 11/820,444 entitled “DIKETO ACIDS    WITH NUCLEOBASE SCAFFOLDS: ANTI-HIV REPLICATION INHIBITORS TARGETED    AT HIV INTEGRASE” filed on Jun. 19, 2007 in the name of Nair, Vasu    et al., published on Nov. 8, 2007 as U.S. Publication No.    20070259823 and assigned to the University of Georgia Research    Foundation, Inc.-   U.S. patent application Ser. No. 11/047,229 entitled “DIKETO ACIDS    WITH NUCLEOBASE SCAFFOLDS: ANTI-HIV REPLICATION INHIBITORS TARGETED    AT HIV INTEGRASE” filed on Jan. 31, 2005 in the name of Nair, Vasu    et al., published on Aug. 3, 2006 as U.S. Publication No.    20060172973.-   U.S. patent application Ser. No. 11/827,959 entitled “PYRIDINONE    DIKETO ACIDS: INHIBITORS OF HIV REPLICATION” filed on Jul. 13, 2007    in the name of Nair, Vasu et al., published on Jan. 24, 2008 as U.S.    Publication No. 20080020010 and assigned to the University of    Georgia Research Foundation, Inc.

Additional integrase inhibitors include L-870,810 (Merck), INH-001(Inhibitex), L870810 (Merck), PL-2500, composed of pryidoxal1-5-phosphate derivatives (Procyon) monophores (Sunesis), V-165 (RegaInstitute, Belgium), Mycelium integrasone (a fungal polyketide, Merck),GS 9224 (Gilead Sciences), AVX-I (Avexa), ITI-367, an oxadiazolpre-integrase inhibitor (George Washington University), GSK364735(GSK/Shionogi), GS-9160 (GSK), S-1360 (Shionogi-GlaxoSmithKlinePharmaceuticals LLC), RSC 1838 (GSK/Shionogi), GS-9137 (taken alone orwith Norvir) (Gilead), MK-2048 (Merck), S/GSK 1349572 and S/GSK 1265744(no need for a PK booster) (GSK/Shionogi),6-(3-chloro-2-fluorobenzyl)-1-[(2S)-1-hydroxy-3-methylbutan-2-yl]-7-methoxy-4-oxo-1,4-dihydroquinoline-3-carboxylicacid (U.S. Patent Application Publication No. 20090018162), S-1360,L-870810, Raltegravir, C-2507 (Merck), BMS 538158 (Bristol MyersSquibb), and L-900564 (Merck).

The structure of L-900564 is shown below:

-   Nair et al., J Med Chem. 2006 Jan. 26; 49(2): 445-447, discloses the    following integrase inhibitors:

Additional integrase inhibitors are disclosed in Pais et al., J MedChem. 2002 Jul. 18; 45(15):3184-94.

Several integrase inhibitors are peptides, including those disclosed inDivita et al., Antiviral Research, Volume 71, Issues 2-3, September2006, Pages 260-267.

Another integrase inhibitor that can be used in the methods of treatmentdescribed herein include 118-D-24, which is disclosed, for example, inVatakis, Journal of Virology, April 2009, p. 3374-3378, Vol. 83, No. 7.

Additional integrase inhibitors include those described in McKeel etal., “Dynamic Modulation of HIV-1 Integrase Structure and Function byCellular LEDGF Protein, JBC Papers in Press. Published on Sep. 18, 2008as Manuscript M805843200.

Other representative integrase inhibitors include dicaffeoylquinic acids(DCQAs), such as those disclosed in Zhu et al., “Irreversible Inhibitionof Human Immunodeficiency Virus Type 1 Integrase by DicaffeoylquinicAcids,” Journal of Virology, April 1999, p. 3309-3316, Vol. 73, No. 4.

There are also various nucleoside compounds active as integraseinhibitors, including those disclosed in Mazumder, A., N. Neamati, J. P.Sommadossi, G. Gosselin, R. F. Schinazi, J. L. Imbach, and Y. Pommier.1996. Effects of nucleotide analogues on human immunodeficiency virustype 1 integrase. Mol. Pharmacol. 49:621-628.

Protease Inhibitors

Protease inhibitors treat or prevent HIV infection by preventing viralreplication. They act by inhibiting the activity of HIV protease, anenzyme that cleaves nascent proteins for final assembly of new virons.Examples are shown in the table that follows.

HIV Therapies: Protease Inhibitors (PIs)

Brand Generic Experimental Pharmaceutical Name Name Abbreviation CodeCompany Invirase ® saquinavir SQV (HGC) Ro-31-8959 Hoffmann-La Roche(Hard Gel Cap) Fortovase ® saquinavir SQV (SGC) Hoffmann-La Roche (SoftGel Cap) Norvir ® Ritonavir RTV ABT-538 Abbott Laboratories Crixivan ®Indinavir IDV MK-639 Merck & Co. Viracept ® Nelfinavir NFV AG-1343Pfizer Agenerase ® amprenavir APV 141W94 GlaxoSmithKline or VX-478Kaletra ® lopinavir + LPV ABT-378/r Abbott Laboratories ritonavirLexiva ® fosamprenavir GW-433908 GlaxoSmithKline or VX-175 Aptivus ®tripanavir TPV PNU-140690 Boehringer Ingelheim Reyataz ® atazanavirBMS-232632 Bristol-Myers Squibb brecanavir GW640385 GlaxoSmithKlinePrezista ™ darunavir TMC114 Tibotec

HIV Therapies: Other Classes of Drugs

Brand Generic Experimental Pharmaceutical Name Name Abbreviation CodeCompany Viread ™ tenofovir TDF or Gilead Sciences disoproxil Bis(POC)fumarate (DF) PMPA GS-7340 Tenofovir TAF Gilead Sciences alafenamidefumarate

Cellular Inhibitors

Brand Generic Experimental Pharmaceutical Name Name Abbreviation CodeCompany Droxia ® hydroxyurea HU Bristol-Myers Squibb

HIV Therapies: Immune-Based Therapies

Brand Generic Experimental Pharmaceutical Name Name Abbreviation CodeCompany Proleukin ® aldesleukin, or IL-2 Chiron CorporationInterleukin-2 Remune ® HIV-1 AG1661 The Immune Response Immunogen, orCorporation Salk vaccine HE2000 HollisEden Pharmaceuticals

III. Combination or Alternation HIV-Agents

In general, during alternation therapy, an effective dosage of eachagent is administered serially, whereas in combination therapy, aneffective dosage of two or more agents is administered together. Inalternation therapy, for example, one or more first agents can beadministered in an effective amount for an effective time period totreat the viral infection, and then one or more second agentssubstituted for those first agents in the therapy routine and likewisegiven in an effective amount for an effective time period.

The dosages will depend on such factors as absorption, biodistribution,metabolism and excretion rates for each drug as well as other factorsknown to those of skill in the art. It is to be noted that dosage valueswill also vary with the severity of the condition to be alleviated. Itis to be further understood that for any particular subject, specificdosage regimens and schedules should be adjusted over time according tothe individual need and the professional judgment of the personadministering or supervising the administration of the compositions.

Examples of suitable dosage ranges for anti-HIV compounds, including theJAK inhibitors described herein, can be found in the scientificliterature and in the Physicians Desk Reference. Many examples ofsuitable dosage ranges for other compounds described herein are alsofound in public literature or can be identified using known procedures.These dosage ranges can be modified as desired to achieve a desiredresult.

IV. Pharmaceutical Compositions

Humans suffering from effects caused by HIV infection can be treated byadministering to the patient an effective amount of the compositionsdescribed above, in the presence of a pharmaceutically acceptablecarrier or diluent, for any of the indications or modes ofadministration as described in detail herein. The active materials canbe administered by any appropriate route, for example, orally,parenterally, enterally, intravenously, intradermally, subcutaneously,transdermally, intranasally or topically, in liquid or solid form.

The active compounds are included in the pharmaceutically acceptablecarrier or diluent in an amount sufficient to deliver to a patient atherapeutically effective amount of compound to inhibit viralpropagation in vivo, especially HIV propagation, without causing serioustoxic effects in the treated patient. While not wishing to be bound to aparticular theory, it is believed that the TREM-1 inhibitors willinhibit HIV-1-induced activation of mature monocytes and macrophages,therein 1) reducing permissiveness of infection of bystander cells byreduction of autocrine and paracrine pro-inflammatory events inmonocytes/macrophages, 2) reduce the amount of HIV-1 produced perinfected macrophage, 3) prevent inflammatory and activation driventrafficking of CD14⁺/CD16⁺ monocytes across the blood-brain-barrier, 4)reduce reservoir size/purge myeloid-derived viral sanctuaries byinhibition of myeloid-driven inflammation that promotes reservoirmaintenance, and 5) reduce or eliminate HIV-induced CNS infection andHIV-associated neurocognitive dysfunction by conferring potent, specificinhibition of perivascular macrophage localized HIV-induced activation.

HIVinfection, which is similar in pathology to HIV-2 infection, inducesa significant increase in TNF-α production in HIV-infected macrophages,for both acute and chronic HIV-1 infection. Increase in TNF-α productionis associated with disease progression and viral persistence includingmaintenance of viral reservoirs, which prevents eradication of HIV-1.TREM-1 inhibitors inhibit TNF-α production. Thereby, TREM-1 inhibitorscan be useful in inhibiting the HIV-induced TNF-α production, therebytreating, preventing, or eradicating HIV-1 or HIV-2 infection.

By “inhibitory amount” is meant an amount of active ingredientsufficient to exert an inhibitory effect as measured by, for example, anassay such as the ones described herein.

A preferred dose of the compound for all the above-mentioned conditionswill be in the range from about 1 to 75 mg/kg, preferably 1 to 20 mg/kg,of body weight per day, more generally 0.1 to about 100 mg per kilogrambody weight of the recipient per day. The effective dosage range of thepharmaceutically acceptable derivatives can be calculated based on theweight of the parent nucleoside or other agent to be delivered. If thederivative exhibits activity in itself, the effective dosage can beestimated as above using the weight of the derivative, or by other meansknown to those skilled in the art.

The compounds are conveniently administered in unit any suitable dosageform, including but not limited to one containing 7 to 3,000 mg,preferably 70 to 1,400 mg of active ingredient per unit dosage form. Anoral dosage of 50 to 1,000 mg is usually convenient.

Ideally, the active ingredient should be administered to achieve peakplasma concentrations of the active compound of from about 0.02 to 70micromolar, preferably about 0.5 to 10 micromolar. This may be achieved,for example, by the intravenous injection of a 0.1 to 25% solution ofthe active ingredient, optionally in saline, or administered as a bolusof the active ingredient.

The concentration of active compound in the drug composition will dependon absorption, distribution, metabolism and excretion rates of the drugas well as other factors known to those of skill in the art. It is to benoted that dosage values will also vary with the severity of thecondition to be alleviated. It is to be further understood that for anyparticular subject, specific dosage regimens should be adjusted overtime according to the individual need and the professional judgment ofthe person administering or supervising the administration of thecompositions, and that the concentration ranges set forth herein areexemplary only and are not intended to limit the scope or practice ofthe claimed composition. The active ingredient may be administered atonce, or may be divided into a number of smaller doses to beadministered at varying intervals of time.

A preferred mode of administration of the active compound is oral. Oralcompositions will generally include an inert diluent or an ediblecarrier. They may be enclosed in gelatin capsules or compressed intotablets. For the purpose of oral therapeutic administration, the activecompound can be incorporated with excipients and used in the form oftablets, troches, or capsules. Pharmaceutically compatible bind agents,and/or adjuvant materials can be included as part of the composition.

The tablets, pills, capsules, troches and the like can contain any ofthe following ingredients, or compounds of a similar nature: a bindersuch as microcrystalline cellulose, gum tragacanth or gelatin; anexcipient such as starch or lactose, a disintegrating agent such asalginic acid, Primogel, or corn starch; a lubricant such as magnesiumstearate or Sterotes; a glidant such as colloidal silicon dioxide; asweetening agent such as sucrose or saccharin; or a flavoring agent suchas peppermint, methyl salicylate, or orange flavoring. When the dosageunit form is a capsule, it can contain, in addition to material of theabove type, a liquid carrier such as a fatty oil. In addition, dosageunit forms can contain various other materials which modify the physicalform of the dosage unit, for example, coatings of sugar, shellac, orother enteric agents.

The compounds can be administered as a component of an elixir,suspension, syrup, wafer, chewing gum or the like. A syrup may contain,in addition to the active compounds, sucrose as a sweetening agent andcertain preservatives, dyes and colorings and flavors.

The compounds or their pharmaceutically acceptable derivative or saltsthereof can also be mixed with other active materials that do not impairthe desired action, or with materials that supplement the desiredaction, such as antibiotics, antifungals, antiinflammatories, proteaseinhibitors, or other nucleoside or non-nucleoside antiviral agents, asdiscussed in more detail above. Solutions or suspensions used forparental, intradermal, subcutaneous, or topical application can includethe following components: a sterile diluent such as water for injection,saline solution, fixed oils, polyethylene glycols, glycerine, propyleneglycol or other synthetic solvents; antibacterial agents such as benzylalcohol or methyl parabens; antioxidants such as ascorbic acid or sodiumbisulfite; chelating agents such as ethylenediaminetetraacetic acid;buffers such as acetates, citrates or phosphates and agents for theadjustment of tonicity such as sodium chloride or dextrose. The parentalpreparation can be enclosed in ampoules, disposable syringes or multipledose vials made of glass or plastic.

If administered intravenously, preferred carriers are physiologicalsaline or phosphate buffered saline (PBS).

Liposomal suspensions (including liposomes targeted to infected cellswith monoclonal antibodies to viral antigens) are also preferred aspharmaceutically acceptable carriers, these may be prepared according tomethods known to those skilled in the art, for example, as described inU.S. Pat. No. 4,522,811. For example, liposome formulations may beprepared by dissolving appropriate lipid(s) (such as stearoylphosphatidyl ethanolamine, stearoyl phosphatidyl choline, arachadoylphosphatidyl choline, and cholesterol) in an inorganic solvent that isthen evaporated, leaving behind a thin film of dried lipid on thesurface of the container. An aqueous solution of the active compound orits monophosphate, diphosphate, and/or triphosphate derivatives is thenintroduced into the container. The container is then swirled by hand tofree lipid material from the sides of the container and to disperselipid aggregates, thereby forming the liposomal suspension.

In one embodiment, the composition is a co-formulated pill, tablet, orother oral drug delivery vehicle including one or more of the JAKinhibitors described herein, and optionally including one or moreadditional antiviral agents.

In another embodiment, the JAK inhibitors described herein areco-formulated with ATRIPLA® (efavirenz 600 mg/emtricitabine [(−)-FTC]200 mg/tenofovir disoproxil fumarate 300 mg), and, optionally, with athymidine nRTI such as AZT and a guanine nRTI such as Abacavir (ABC) (ora compound such as DAPD which is deaminated in vivo to form a guaninenRTI, in this case, DXG). Because efavirenz is an NNRTI, tenofovir is anadenine nRTI, (−)-FTC is a cytosine nRTI, and AZT and d4T are thymidinenRTIs, and Abacavir is a guanine nRTI, the combination of thecoformulated compounds will provide, in addition to the JAK inhibitors,all four bases (ACTG) plus an additional agent capable of interactingwith HIV in a different mechanism.

Controlled Release Formulations

All of the U.S. patents cited in this section on controlled releaseformulations are incorporated by reference in their entirety.

In one embodiment, the TREM-inhibitors, and, optionally, other anti-HIVcompounds, are loaded into liposomes, niosomes, and/or micelles,including but not limited to sterically stabilized phospholipidnanomicelles (SSM), sterically stabilized mixed micelles (SSMM), orsterically-stabilized liposomes (SSL), to achieve an improved biologicaleffect in vivo relative to their being administered without being loadedinto these micelles.

The field of biodegradable polymers has developed rapidly since thesynthesis and biodegradability of polylactic acid was reported byKulkarni et al., in 1966 (“Polylactic acid for surgical implants,” Arch.Surg., 93:839). Examples of other polymers which have been reported asuseful as a matrix material for delivery devices include polyanhydrides,polyesters such as polyglycolides and polylactide-co-glycolides,polyamino acids such as polylysine, polymers and copolymers ofpolyethylene oxide, acrylic terminated polyethylene oxide, polyamides,polyurethanes, polyorthoesters, polyacrylonitriles, andpolyphosphazenes. See, for example, U.S. Pat. Nos. 4,891,225 and4,906,474 to Langer (polyanhydrides), U.S. Pat. No. 4,767,628 toHutchinson (polylactide, polylactide-co-glycolide acid), and U.S. Pat.No. 4,530,840 to Tice, et al. (polylactide, polyglycolide, andcopolymers). See also U.S. Pat. No. 5,626,863 to Hubbell, et al whichdescribes photopolymerizable biodegradable hydrogels as tissuecontacting materials and controlled release carriers (hydrogels ofpolymerized and crosslinked macromers comprising hydrophilic oligomershaving biodegradable monomeric or oligomeric extensions, which are endcapped monomers or oligomers capable of polymerization andcrosslinking); and PCT WO 97/05185 filed by Focal, Inc. directed tomultiblock biodegradable hydrogels for use as controlled release agentsfor drug delivery and tissue treatment agents.

Degradable materials of biological origin are well known, for example,crosslinked gelatin. Hyaluronic acid has been crosslinked and used as adegradable swelling polymer for biomedical applications (U.S. Pat. No.4,957,744 to Della Valle et. al.; (1991) “Surface modification ofpolymeric biomaterials for reduced thrombogenicity,” Polym. Mater. Sci.Eng., 62:731 735]).

Many dispersion systems are currently in use as, or being explored foruse as, carriers of substances, particularly biologically activecompounds. Dispersion systems used for pharmaceutical and cosmeticformulations can be categorized as either suspensions or emulsions.Suspensions are defined as solid particles ranging in size from a fewmanometers up to hundreds of microns, dispersed in a liquid medium usingsuspending agents. Solid particles include microspheres, microcapsules,and nanospheres. Emulsions are defined as dispersions of one liquid inanother, stabilized by an interfacial film of emulsifiers such assurfactants and lipids. Emulsion formulations include water in oil andoil in water emulsions, multiple emulsions, microemulsions,microdroplets, and liposomes. Microdroplets are unilamellar phospholipidvesicles that consist of a spherical lipid layer with an oil phaseinside, as defined in U.S. Pat. Nos. 4,622,219 and 4,725,442 issued toHaynes. Liposomes are phospholipid vesicles prepared by mixingwater-insoluble polar lipids with an aqueous solution. The unfavorableentropy caused by mixing the insoluble lipid in the water produces ahighly ordered assembly of concentric closed membranes of phospholipidwith entrapped aqueous solution.

U.S. Pat. No. 4,938,763 to Dunn, et al., discloses a method for formingan implant in situ by dissolving a nonreactive, water insolublethermoplastic polymer in a biocompatible, water soluble solvent to forma liquid, placing the liquid within the body, and allowing the solventto dissipate to produce a solid implant. The polymer solution can beplaced in the body via syringe. The implant can assume the shape of itssurrounding cavity. In an alternative embodiment, the implant is formedfrom reactive, liquid oligomeric polymers which contain no solvent andwhich cure in place to form solids, usually with the addition of acuring catalyst.

A number of patents disclose drug delivery systems that can be used toadminister the combination of antiviral agents, or prodrugs thereof.U.S. Pat. No. 5,749,847 discloses a method for the delivery ofnucleotides into organisms by electrophoration. U.S. Pat. No. 5,718,921discloses microspheres comprising polymer and drug dispersed therewithin. U.S. Pat. No. 5,629,009 discloses a delivery system for thecontrolled release of bioactive factors. U.S. Pat. No. 5,578,325discloses nanoparticles and microparticles of non-linear hydrophilichydrophobic multiblock copolymers. U.S. Pat. No. 5,545,409 discloses adelivery system for the controlled release of bioactive factors. U.S.Pat. No. 5,494,682 discloses ionically cross-linked polymericmicrocapsules.

U.S. Pat. No. 5,728,402 to Andrx Pharmaceuticals, Inc. describes acontrolled release formulation that includes an internal phase, whichcomprises the active drug, its salt or prodrug, in admixture with ahydrogel forming agent, and an external phase which comprises a coatingwhich resists dissolution in the stomach. U.S. Pat. Nos. 5,736,159 and5,558,879 to Andrx Pharmaceuticals, Inc. discloses a controlled releaseformulation for drugs with little water solubility in which a passagewayis formed in situ. U.S. Pat. No. 5,567,441 to Andrx Pharmaceuticals,Inc. discloses a once-a-day controlled release formulation. U.S. Pat.No. 5,508,040 discloses a multiparticulate pulsatile drug deliverysystem. U.S. Pat. No. 5,472,708 discloses a pulsatile particle baseddrug delivery system. U.S. Pat. No. 5,458,888 describes a controlledrelease tablet formulation, which can be made using a blend having aninternal drug containing phase and an external phase, which comprises apolyethylene glycol polymer, which has a weight average molecular weightof from 3,000 to 10,000. U.S. Pat. No. 5,419,917 discloses methods forthe modification of the rate of release of a drug form a hydrogel whichis based on the use of an effective amount of a pharmaceuticallyacceptable ionizable compound that is capable of providing asubstantially zero-order release rate of drug from the hydrogel. U.S.Pat. No. 5,458,888 discloses a controlled release tablet formulation.

U.S. Pat. No. 5,641,745 to Elan Corporation, plc discloses a controlledrelease pharmaceutical formulation, which comprises the active drug in abiodegradable polymer to form microspheres or nanospheres. Thebiodegradable polymer is suitably poly-D,L-lactide or a blend ofpoly-D,L-lactide and poly-D,L-lactide-co-glycolide. U.S. Pat. No.5,616,345 to Elan Corporation plc describes a controlled absorptionformulation for once a day administration that includes the activecompound in association with an organic acid, and a multi-layer membranesurrounding the core and containing a major proportion of apharmaceutically acceptable film-forming, water insoluble syntheticpolymer and a minor proportion of a pharmaceutically acceptablefilm-forming water soluble synthetic polymer. U.S. Pat. No. 5,641,515discloses a controlled release formulation based on biodegradablenanoparticles. U.S. Pat. No. 5,637,320 discloses a controlled absorptionformulation for once a day administration. U.S. Pat. Nos. 5,580,580 and5,540,938 are directed to formulations and their use in the treatment ofneurological diseases. U.S. Pat. No. 5,533,995 is directed to a passivetransdermal device with controlled drug delivery. U.S. Pat. No.5,505,962 describes a controlled release pharmaceutical formulation.

Prodrug Formulations

The TREM-1 inhibitors, as well as the nucleosides or other compoundswhich are described herein for use in combination or alternation therapywith the TREM-1 inhibitors or their related compounds, can beadministered as an acylated prodrug or a nucleotide prodrug, asdescribed in detail below. Nanoformulations of TREM-1 inhibitors, orflurochrome-conjugated TREM-1 inhibitors at any and all proteins withinthe TREM-1 inhibitors are within the scope of the invention describedherein. Prodrugs designed to modify the peptide sequences describedherein are also within the scope of the invention.

Any of the TREM-1 inhibitors, nucleosides, nucleotides or othercompounds described herein that contain a hydroxyl or amine function canbe administered as a nucleotide prodrug to increase the activity,bioavailability, stability or otherwise alter the properties of thenucleoside. A number of nucleotide prodrug ligands are known. Ingeneral, alkylation, acylation or other lipophilic modification of thehydroxyl group of the compound or of the mono, di or triphosphate of thenucleoside will increase the stability of the nucleotide. Examples ofsubstituent groups that can replace one or more hydrogens on thephosphate moiety or hydroxyl are alkyl, aryl, steroids, carbohydrates,including sugars, 1,2-diacylglycerol and alcohols. Many are described inR. Jones and N. Bischofberger, Antiviral Research, 27 (1995) 1 17. Anyof these can be used in combination with the disclosed nucleosides orother compounds to achieve a desire effect.

The active nucleoside or other hydroxyl containing compound can also beprovided as an ether lipid (and particularly a 5′-ether lipid for anucleoside), as disclosed in the following references, Kucera, L. S., N.Iyer, E. Leake, A. Raben, Modest E. K., D. L. W., and C. Piantadosi.1990. “Novel membrane-interactive ether lipid analogs that inhibitinfectious HIV-1 production and induce defective virus formation.” AIDSRes. Hum. Retroviruses. 6:491 501; Piantadosi, C., J. Marasco C. J., S.L. Morris-Natschke, K. L. Meyer, F. Gumus, J. R. Surles, K. S. Ishaq, L.S. Kucera, N. Iyer, C. A. Wallen, S. Piantadosi, and E. J. Modest. 1991.“Synthesis and evaluation of novel ether lipid nucleoside conjugates foranti-HIV activity.” J. Med. Chem. 34:1408.1414; Hosteller, K. Y., D. D.Richrnan, D. A. Carson, L. M. Stuhmiller, G. M. T. van Wijk, and H. vanden Bosch. 1992. “Greatly enhanced inhibition of human immunodeficiencyvirus type 1 replication in CEM and HT4-6C cells by 3′-deoxythymidinediphosphate dimyristoylglycerol, a lipid prodrug of 3′-deoxythymidine.”Antimicrob. Agents Chemother. 36:2025.2029; Hostetler, K. Y., L. M.Stuhmiller, H. B. Lenting, H. van den Bosch, and D. D. Richman, 1990.“Synthesis and antiretroviral activity of phospholipid analogs ofazidothymidine and other antiviral nucleosides.” J. Biol. Chem.265:61127.

Nonlimiting examples of U.S. patents that disclose suitable lipophilicsubstituents that can be covalently incorporated into the nucleoside orother hydroxyl or amine containing compound, preferably at the 5′-OHposition of the nucleoside or lipophilic preparations, include U.S. Pat.No. 5,149,794 (Sep. 22, 1992, Yatvin et al.); U.S. Pat. No. 5,194,654(Mar. 16, 1993, Hostetler et al., U.S. Pat. No. 5,223,263 (Jun. 29,1993, Hostetler et al.); U.S. Pat. No. 5,256,641 (Oct. 26, 1993, Yatvinet al.); U.S. Pat. No. 5,411,947 (May 2, 1995, Hostetler et al.); U.S.Pat. No. 5,463,092 (Oct. 31, 1995, Hostetler et al.); U.S. Pat. No.5,543,389 (Aug. 6, 1996, Yatvin et al.); U.S. Pat. No. 5,543,390 (Aug.6, 1996, Yatvin et al.); U.S. Pat. No. 5,543,391 (Aug. 6, 1996, Yatvinet al.); and U.S. Pat. No. 5,554,728 (Sep. 10, 1996; Basava et-al.),Foreign patent applications that disclose lipophilic substituents thatcan be attached to the nucleosides of the present invention, orlipophilic preparations, include WO 89/02733, WO 90/00555, WO 91/16920,WO 91/18914, WO 93/00910, WO 94/26273, WO 96/15132, EP 0 350 287, EP93917054.4, and WO 91/19721.

Nonlimiting examples of nucleotide prodrugs are described in thefollowing references: Ho, D. H. W. (1973) “Distribution of Kinase anddeaminase of 1-β-D-arabinofuranosylcytosine in tissues of man and muse.”Cancer Res. 33, 2816 2820; Holy, A. (1993) Isopolar phosphorous-modifiednucleotide analogues,” In: De Clercq (Ed.), Advances in Antiviral DrugDesign, Vol. I, JAI Press, pp. 179 231; Hong, C. I., Nechaev, A., andWest, C. R. (1979a) “Synthesis and antitumor activity of13-D-arabino-furanosylcytosine conjugates of cortisol and cortisone.”Biochem. Biophys. Rs. Commun. 88, 1223 1229; Hong, C. I., Nechaev, A.,Kirisits, A. J. Buchheit, D. J. and West, C. R. (1980) “Nucleosideconjugates as potential antitumor agents. 3. Synthesis and antitumoractivity of 1-(P3-D-arabinofuranosyl)cytosine conjugates ofcorticosteroids and selected lipophilic alcohols.” J. Med. Chem. 28, 171177; Hosteller, K. Y., Stuhmiller, L. M., Lenting, H. B. M. van denBosch, H. and Richman J Biol. Chem. 265, 6112 6117; Hosteller, K. Y.,Carson, D. A. and Richman, D. D. (1991); “Phosphatidylazidothymidine:mechanism of antiretroviral action in CEM cells.” J. Biol Chem. 266,11714 11717; Hosteller, K. Y., Korba, B. Sridhar, C., Gardener, M.(1994a) “Antiviral activity of phosphatidyl-dideoxycytidine in hepatitisB-infected cells and enhanced hepatic uptake in mice.” Antiviral Res.24, 59 67; Hosteller, K. Y., Richman, D. D., Sridhar. C. N. Felgner, P.L. Felgner, J., Ricci, J., Gardener, M. F. Selleseth, D. W. and Ellis,M. N. (1994b) “Phosphatidylazidothymidine and phosphatidyl-ddC:Assessment of uptake in mouse lymphoid tissues and antiviral activitiesin human immunodeficiency virus-infected cells and in rauscher leukemiavirus-infected mice.” Antimicrobial Agents Chemother. 38, 2792 2797;Hunston, R. N., Jones, A. A. McGuigan, C., Walker, R. T., Balzarini, J.,and DeClercq, E. (1984) “Synthesis and biological properties of somecyclic phosphotriesters derived from 2′-deoxy-5-fluorouridine.” J. Med.Chem. 27,440 444; Ji, Y. H., Moog, C., Schmitt, G., Bischoff, P. andLuu, B. (1990); “Monophosphoric acid esters of 7-β-hydroxycholesteroland of pyrimidine nucleoside as potential antitumor agents: synthesisand preliminary evaluation of antitumor activity.” J. Med. Chem. 33 22642270; Jones, A. S., McGuigan, C., Walker, R. T., Balzarini, J. andDeClercq, E. (1984) “Synthesis, properties, and biological activity ofsome nucleoside cyclic phosphoramidates.” J. Chem. Soc. Perkin Trans. I,1471 1474; Juodka, B. A. and Smart, J. (1974) “Synthesis ofdiribonucleoside phosph (P.fwdarw.N) amino acid derivatives.” Coll.Czech. Chem. Comm. 39, 363 968; Kataoka, S., Imai, J., Yamaji, N., Kato,M., Saito, M., Kawada, T. and Imai, S. (1989) “Alkylated cAMPderivatives; selective synthesis and biological activities.” NucleicAcids Res. Sym. Ser. 21, 1 2; Kataoka, S., Uchida, “(cAMP) benzyl andmethyl triesters.” Heterocycles 32, 1351 1356; Kinchington, D., Harvey,J. J., O'Connor, T. J., Jones, B. C. N. M., Devine, K. G.,Taylor-Robinson D., Jeffries, D. J. and McGuigan, C. (1992) “Comparisonof antiviral effects of zidovudine phosphoramidate andphosphorodiamidate derivatives against HIV and ULV in vitro.” AntiviralChem. Chemother. 3, 107 112; Kodama, K., Morozumi, M., Saithoh, K. I.,Kuninaka, H., Yosino, H. and Saneyoshi, M. (1989) “Antitumor activityand pharmacology of 1-β-D-arabinofuranosylcytosine-5′-stearylphosphate;an orally active derivative of 1-β-Darabinofuranosylcytosine.” Jpn. J.Cancer Res. 80, 679 685; Korty, M. and Engels, J. (1979) “The effects ofadenosine- and guanosine 3′,5′ phosphoric and acid benzyl esters onguinea-pig ventricular myocardium.” Naunyn-Schmiedeberg's Arch.Pharmacol. 310, 103 111; Kumar, A., Goe, P. L., Jones, A. S. Walker, R.T. Balzarini, J. and DeClercq, E. (1990) “Synthesis and biologicalevaluation of some cyclic phosphoramidate nucleoside derivatives.” J.Med. Chem, 33, 2368 2375; LeBec, C., and Huynh-Dinh, T. (1991)“Synthesis of lipophilic phosphate triester derivatives of5-fluorouridine an arabinocytidine as anticancer prodrugs.” TetrahedronLett. 32, 6553 6556; Lichtenstein, J., Barner, H. D. and Cohen, S. S.(1960) “The metabolism of exogenously supplied nucleotides byEscherichia coli.,” J. Biol. Chem. 235, 457 465; Lucthy, J., VonDaeniken, A., Friederich, J. Manthey, B., Zweifel, J., Schlatter, C. andBenn, M. H. (1981) “Synthesis and toxicological properties of threenaturally occurring cyanoepithioalkanes”. Mitt. Geg. Lebensmittelunters.Hyg. 72, 131 133 (Chem. Abstr. 95, 127093); McGigan, C. Tollerfield, S.M. and Riley, P. a. (1989) “Synthesis and biological evaluation of somephosphate triester derivatives of the anti-viral drug Ara.” NucleicAcids Res. 17, 6065 6075; McGuigan, C., Devine, K. G., O'Connor, T. J.,Galpin, S. A., Jeffries, D. J. and Kinchington, D. (1990a) “Synthesisand evaluation of some novel phosphoramidate derivatives of3′-azido-3′-deoxythymidine (AZT) as anti-HIV compounds.” Antiviral Chem.Chemother. 1 107 113; McGuigan, C., O'Connor, T. J., Nicholls, S. R.Nickson, C. and Kinchington, D. (1990b) “Synthesis and anti-HIV activityof some novel substituted dialkyl phosphate derivatives of AZT andddCyd.” Antiviral Chem. Chemother. 1, 355 360; McGuigan, C., Nicholls,S. R., O'Connor, T. J., and Kinchington, D. (1990c) “Synthesis of somenovel dialkyl phosphate derivative of 3′-modified nucleosides aspotential anti-AIDS drugs.” Antiviral Chem. Chemother. 1, 25 33;McGuigan, C., Devin, K. G., O'Connor, T. J., and Kinchington, D. (1991)“Synthesis and anti-HIV activity of some haloalkyl phosphoramidatederivatives of 3′-azido-3′-deoxythylmidine (AZT); potent activity of thetrichloroethyl methoxyalaninyl compound.” Antiviral Res. 15, 255 263;McGuigan, C., Pathirana, R. N., Balzarini, J. and DeClercq, E. (1993b)“Intracellular delivery of bioactive AZT nucleotides by aryl phosphatederivatives of AZT.” J. Med. Chem. 36, 1048 1052.

Alkyl hydrogen phosphate derivatives of the anti-HIV agent AZT may beless toxic than the parent nucleoside analogue. Antiviral Chem.Chemother. 5, 271 277; Meyer, R. B., Jr., Shuman, D. A. and Robins, R.K. (1973) “Synthesis of purine nucleoside 3′,5′-cyclicphosphoramidates.” Tetrahedron Lett. 269 272; Nagyvary, J. Gohil, R. N.,Kirchner, C. R. and Stevens, J. D. (1973) “Studies on neutral esters ofcyclic AMP,” Biochem. Biophys. Res. Commun. 55, 1072 1077; Namane, A.Gouyette, C., Fillion, M. P., Fillion, G. and Huynh-Dinh, T. (1992)“Improved brain delivery of AZT using a glycosyl phosphotriesterprodrug.” J. Med. Chem. 35, 3039 3044; Nargeot, J. Nerbonne, J. M.Engels, J. and Leser, H. A. (1983) Natl. Acad. Sci. U.S.A. 80, 23952399; Nelson, K. A., Bentrude, W. G. Stser, W. N. and Hutchinson, J. P.(1987) “The question of chair-twist equilibria for the phosphate ringsof nucleoside cyclic 3′,5′-monophosphates. ¹HNMR and x-raycrystallographic study of the diastereomers of thymidine phenyl cyclic3′,5′-monophosphate.” J. Am. Chem. Soc. 109, 4058 4064; Nerbonne, J. M.,Richard, S., Nargeot, J. and Lester, H. A. (1984) “New photoactivatablecyclic nucleotides produce intracellular jumps in cyclic AMP and cyclicGMP concentrations.” Nature 301, 74 76; Neumann, J. M., Herv_, M.,Debouzy, J. C., Guerra, F. I., Gouyette, C., Dupraz, B. and Huyny-Dinh,T. (1989) “Synthesis and transmembrane transport studies by NMR of aglucosyl phospholipid of thymidine.” J. Am. Chem. Soc. 111, 4270 4277;Ohno, R., Tatsumi, N., Hirano, M., Imai, K. Mizoguchi, H., Nakamura, T.,Kosaka, M., Takatuski, K., Yamaya, T., Toyama K., Yoshida, T., Masaoka,T., Hashimoto, S., Ohshima, T., Kimura, I., Yamada, K. and Kimura, J.(1991) “Treatment of myelodysplastic syndromes with orally administered1-β-D-arabinouranosylcytosine-5′ stearylphosphate.” Oncology 48, 451455. Palomino, E., Kessle, D. and Horwitz, J. P. (1989) “Adihydropyridine carrier system for sustained delivery of 2′,3′dideoxynucleosides to the brain.” J. Med. Chem. 32, 22 625; Perkins, R.M., Barney, S. Wittrock, R., Clark, P. H., Levin, R. Lambert, D. M.,Petteway, S. R., Serafinowska, H. T., Bailey, S. M., Jackson, S.,Harnden, M. R. Ashton, R., Sutton, D., Harvey, J. J. and Brown, A. G.(1993) “Activity of BRL47923 and its oral prodrug, SB203657A against arauscher murine leukemia virus infection in mice.” Antiviral Res. 20(Suppl. 1). 84; Piantadosi, C., Marasco, C. J., Jr., Norris-Natschke, S.L., Meyer, K. L., Gumus, F., Surles, J. R., lshaq, K. S., Kucera, L. S.Iyer, N., Wallen, C. A., Piantadosi, S. and Modest, E. J. (1991)“Synthesis and evaluation of novel ether lipid nucleoside conjugates foranti-HIV-1 activity.” J. Med. Chem. 34, 1408 1414; Pompon, A., Lefebvre,I., Imbach, J. L., Kahn, S. and Farquhar, D. (1994). “Decompositionpathways of the mono- and bis(pivaloyloxymethyl) esters ofazidothymidine-5′-monophosphate in cell extract and in tissue culturemedium; an application of the ‘on-line ISRP-cleaning HPLC technique.”Antiviral Chem Chemother. 5, 91 98; Postemark, T. (1974) “Cyclic AMP andcyclic GMP.” Annu. Rev. Pharmacol. 14, 23 33; Prisbe, E. J., Martin, J.C. M., McGhee, D. P. C., Barker, M. F., Smee, D. F. Duke, A. E.,Matthews, T. R. and Verheyden, J. P. J. (1986) “Synthesis and antiherpesvirus activity of phosphate an phosphonate derivatives of9-[(1,3-dihydroxy-2-propoxy)methyl]guanine.” J. Med. Chem. 29, 671 675;Pucch, F., Gosselin, G., Lefebvre, I., Pompon, a., Aubertin, A. M. Dim,and Imbach, J. L. (1993) “Intracellular delivery of nucleosidemonophosphate through a reductase-mediated activation process.”Antiviral Res. 22, 155 174; Pugaeva, V. P., Klochkeva, S. I., Mashbits,F. D. and Eizengart, R. S. (1969). “Toxicological assessment and healthstandard ratings for ethylene sulfide in the industrial atmosphere.”Gig. Trf. Prof. Zabol. 14, 47 48 (Chem. Abstr. 72, 212); Robins, R. K.(1984) “The potential of nucleotide analogs as inhibitors of Retroviruses and tumors.” Pharm. Res. 11 18; Rosowsky, A., Kim. S. H., Rossand J. Wick, M. M. (1982) “Lipophilic 5′-(alkylphosphate) esters of1-P3-D-arabinofiiranosylcytosine and its N⁴-acyl and2.2′-anhydro-3′-O-acyl derivatives as potential prodrugs.” J. Med. Chem.25, 171 178; Ross, W. (1961) “Increased sensitivity of the walkerturnout towards aromatic nitrogen mustards carrying basic side chainsfollowing glucose pretreatment.” Biochem. Pharm. 8, 235 240; Ryu, E. K.,Ross, R. J. Matsushita, T., MacCoss, M., Hong, C. I. and West, C. R.(1982). “Phospholipid-nucleoside conjugates. 3. Synthesis andpreliminary biological evaluation of 1-β-D-arabinofuranosylcytosine5′diphosphate [−], 2-diacylglycerols.” J. Med. Chem. 25, 1322 1329;Saffhill, R. and Hume, W. J. (1986) “The degradation of5-iododeoxyuridine and 5-bromoethoxyuridine by serum from differentsources and its consequences for the use of these compounds forincorporation into DNA.” Chem. Biol. Interact. 57, 347 355; Saneyoshi,M., Morozumi, M., Kodama, K., Machida, J., Kuninaka, A. and Yoshino, H.(1980) “Synthetic nucleosides and nucleotides. XVI. Synthesis andbiological evaluations of a series of 1-β-D-arabinofuranosylcytosine5′-alky or arylphosphates.” Chem Pharm. Bull. 28, 2915 2923; Sastry, J.K., Nehete, P. N., Khan, S., Nowak, B. J., Plunkett, W., Arlinghaus, R.B. and Farquhar, D. (1 992) “Membrane-permeable dideoxyuridine5′-monophosphate analogue inhibits human immunodeficiency virusinfection.” Mol. Pharmacol. 41, 441 445; Shaw, J. P., Jones, R. J.Arimilli, M. N., Louie, M. S., Lee, W. A. and Cundy, K. C. (1994) “Oralbioavailability of PMEA from PMEA prodrugs in male Sprague-Dawley rats.”9th Annual AAPS Meeting. San Diego, Calif. (Abstract). Shuto, S., Ueda,S., Imamura, S., Fukukawa, K. Matsuda, A. and Ueda, T. (1987) “A facileone-step synthesis of 5′ phosphatidiylnucleosides by an enzymatictwo-phase reaction.” Tetrahedron Lett. 28, 199 202; Shuto, S. Itoh, H.,Ueda, S., Imamura, S., Kukukawa, K., Tsujino, M., Matsuda, A. and Ueda,T. (1988) Pharm. Bull. 36, 209 217. An example of a useful phosphateprodrug group is the S-acyl-2-thioethyl group, also referred to as“SATE”. Such compounds can be used in the methods described herein.

As used herein, Chikungunya virus is an RNA virus of the genusAlphavirus, and can also be treated using the compounds describedherein.

As used herein, Dengue virus includes the Dengue virus group (Denguevirus, Dengue virus type 1, Dengue virus type 2, Dengue virus type 3,and Dengue virus type 4).

VI. Methods of Treatment

The compositions described herein can be used to treat patients infectedwith HIV-1 and HIV-2, Dengue virus, and Chikungunya virus, to prevent aninfection by these viruses, or to eradicate an infection by theseviruses.

When the treatment of HIV-1 or HIV-2 involves co-administration of theTREM-1 inhibitors described herein and nucleoside antiviral agentsand/or non-thymidine nucleoside antiviral agents, the HIV-1 may alreadyhave developed one or more mutations, such as the M184V, K65R mutationor TAMS. In such a case, the second agent will ideally be selected to beactive against HIV-1 that has these mutations. Methods for selectingappropriate antiretroviral therapy for patients with various mutationsin their HIV-1 are known to those of skill in the art.

When the treatment involves the co-administration of an adenine,cytosine, thymidine, and guanine nucleoside antiviral agent, as well asthe additional antiviral agent(s), ideally the administration is to apatient who has not yet developed any resistance to these antiviralagents or has been off therapy for at least three months. In that case,it may be possible to actually cure an infected patient if the therapycan treat substantially all of the virus, substantially everywhere itresides in the patient. However, even in the case of infection by aresistant virus, the combination therapy should be effective against allknown resistant viral strains, because there is at least one agentcapable of inhibiting such a virus in this combination therapy, andbecause the TREM-1 inhibitors do not function in the same manner as theconventional NRTI, NNRTI, protease inhibitors, entry inhibitors,integrase inhibitors, and the like, and thus remain effective againststrains that have mutated following exposure to these agents.

The compounds can be used in different ways to treat or prevent HIV,and, in one embodiment, to cure an HIV infection. In one embodiment, acombination of a TREM-1 inhibitor as described herein, a macrophagedepleting agent (e.g., clodronate-loaded or bis-phosphonate-loadedliposomes, gadolinium chloride (GdCl)), plus HAART therapy is used. Thestrategy involves reducing viral loads with traditional HAART and TREM-1inhibitor therapy. Then, macrophages are systemically depleted(typically without discrimination for infected versus infectedmacrophages). HAART and TREM-1 inhibitor therapy would be maintainedduring macrophage depletion. Then, treatment with the macrophagedepleting agent is withdrawn, while treatment with HAART and the TREM-1inhibitor is maintained.

In one aspect of this embodiment, HAART is then withdrawn, while TREM-1inhibitor therapy is maintained, optionally while monitoring viralrebound.

In another aspect of this embodiment, both HAART and TREM-1 inhibitortherapy are then withdrawn, optionally while monitoring viral rebound.

In another embodiment, viral loads are reduced with traditionalHAART+TREM-1 inhibitors, specifically one or both of Tofacitinib andJakafi, as described herein. Then, macrophages are systemically depleted(typically without discrimination for infected versus infectedmacrophages) with Boniva or Fosamax (both of these drugs are potentmacrophage depleting agents). HAART+TREM-1 inhibitor therapy ismaintained during macrophage depletion. Then, treatment with themacrophage depleting agent is withdrawn, while treatment with HAART andthe TREM-1 inhibitor is maintained.

In one aspect of this embodiment, HAART is then withdrawn, while TREM-1inhibitor therapy with one or both of Tofacitinib and Jakafi ismaintained, optionally while monitoring viral rebound.

In another aspect of this embodiment, both HAART and TREM-1 inhibitortherapy with one or both of Tofacitinib and Jakafi are then withdrawn,optionally while monitoring viral rebound.

In another embodiment, a combination of a histone deacetylase inhibitor(HDAC inhibitor) or interleukin 7 (IL-7) and HAART and a TREM-1inhibitor is used. One limitation associated with treating HIV is thatwhile it is not fully understood how HIV-1 evades the immune responseand establishes latency in resting cells, it is believed that a varietyof signalling molecules and transcription factors appear to play a role,and thus offer potential targets for intervention. Thus, in thisembodiment, IL-7 is used to confer reactivation of resting cells,effectively flushing HIV-1 out of hiding, and histone deacetylase (HDAC)inhibitors are used to confer reactivation by up regulation of pro-HIVgenes, effectively coaxing virus out from previously resting cells. Inthis manner, latent HIV is eradicated. An example of a reactivationagent that could be used in this manner is panobinostate, which isdescribed, for example, in Lewin, et al., “HIV cure and eradication: howwill we get from the laboratory to effective clinical trials?” AIDS:24Apr. 2011. Representative HDAC inhibitors include Vorinostat, Romidepsin(trade name Istodax), Panobinostat (LBH589), Valproic acid (including Mgvalproate and other salt forms), Belinostat (PXD101), Mocetinostat(MGCD0103), PCI-24781, Entinostat (MS-275), SB939, Resminostat(4SC-201), Givinostat (ITF2357), CUDC-101, AR-42, CHR-2845, CHR-3996,4SC-202, sulforaphane, suberoylanilide hydroxamic acid (SAHA), BML-210,M344, CI-994; CI-994 (Tacedinaline); BML-210; M344; MGCD0103(Mocetinostat); and Tubastatin A. Additional HDAC inhibitors aredescribed in U.S. Pat. No. 7,399,787.

The strategy involves reducing viral loads with traditional HAART andTREM-1 inhibitor therapy. Then, the patient is treated with areactivation agent (as defined in Lewin et al., supra), such aspanobinostat.

In one aspect of this embodiment, both HAART and TREM-1 inhibitortherapy are maintained during reactivation, and in another aspect ofthis embodiment, HAART, but not TREM-1 inhibitor therapy, is maintainedduring reactivation.

Treatment with the reactivation agent is then withdrawn, whilecontinuing treatment with HAART and one or more TREM-1 inhibitors, suchas Tofacitinib and Jakafi as defined herein.

In one aspect of this embodiment, HAART is then withdrawn, while TREM-1inhibitor therapy is maintained, optionally while monitoring viralrebound.

In another aspect of this embodiment, both HAART and TREM-1 inhibitortherapy are then withdrawn, optionally while monitoring viral rebound.

In another embodiment, the TREM-1 inhibitors are administered to apatient before, during, or after administration of a vaccine and/or animmunostimulant. The use of immunostimulants can provide an optimalantiretroviral regimen. The immunostimulatory treatments include, butare not limited to, therapies from two functional classes: 1) agentsthat target actively replicating cells and 2) agents activating latentlyinfected cells.

In addition to the TREM-1 inhibitors and immunomodulatory agents, HAARTcan also be provided. The TREM-1 inhibitors, optionally withco-administered HAART, can suppress virus to undetectable or virtuallyundetectable levels. The addition of an immunomodulatory therapy thatspecifically targets viral reservoirs can, ideally, lead to a cure, orat least remove virus from one or more viral reservoirs.

Immunostimulants

The term “immunostimulant” is used herein to describe a substance whichevokes, increases and/or prolongs an immune response to an antigen.While the present application distinguishes between an “antigen” and an“immunostimulant” it should be noted that this is merely for reasons ofclarity and ease of description. It should be understood that theimmunostimulant could have, and in many cases preferably has, antigenicpotential itself.

Immunomodulatory agents modulate the immune system, and, as used herein,immunostimulants are also referred to as immunomodulatory agents, whereit is understood that the desired modulation is to stimulate the immunesystem.

There are two main categories of immunostimulants, specific andnon-specific. Specific immunostimulants provide antigenic specificity inimmune response, such as vaccines or any antigen, and non-specificimmunostimulants act irrespective of antigenic specificity to augmentimmune response of other antigen or stimulate components of the immunesystem without antigenic specificity, such as adjuvants and non-specificimmunostimulators.

Examples of immunostimulants include levamisole, thalidomide, erythemanodosum leprosum, BCG, cytokines such as interleukins or interferons,including recombinant cytokines and interleukin 2 (aldeslukin), 3D-MPL,QS21, CpG ODN 7909, miltefosine, anti-PD-1 or PD-1 targeting drugs, andacid (DCA, a macrophage stimulator), imiquimod and resiquimod (whichactivate immune cells through the toll-like receptor 7), chlorooxygencompounds such as tetrachlorodecaoxide (TCDO), agonistic CD40antibodies, soluble CD40L, 4-1BB:4-1BBL agonists, OX40 agonists, TLRagonists, moieties that deplete regulatory T cells, arabinitol-ceramide,glycerol-ceramide, 6-deoxy and 6-sulfono-myo-insitolceramide, iNKTagonists, TLR agonists.

WF 10 [Immunokine, Macrokine] is a 1:10 dilution of tetrachlorodecaoxide(TCDO) formulated for intravenous injection. WF 10 specifically targetsmacrophages, and modulates disease-related up-regulation of immuneresponses in vivo.

3D-MPL is an immunostimulant derived from the lipopolysaccharide (LPS)of the Gram-negative bacterium Salmonella minnesota. MPL has beendeacylated and is lacking a phosphate group on the lipid A moiety. Thischemical treatment dramatically reduces toxicity while preserving theimmunostimulant properties (Ribi, 1986). Ribi Immunochemistry producesand supplies MPL to GSK-Biologicals.

QS21: is a natural saponin molecule extracted from the bark of the SouthAmerican tree Quillaja saponaria Molina. A purification techniquedeveloped to separate the individual saponins from the crude extracts ofthe bark, permitted the isolation of the particular saponin, QS21, whichis a triterpene glycoside demonstrating stronger adjuvant activity andlower toxicity as compared with the parent component. QS21 has beenshown to activate MHC class I restricted CTLs to several subunit Ags, aswell as to stimulate Ag specific lymphocytic proliferation (Kensil,1992). Aquila (formally Cambridge Biotech Corporation) produces andsupplies QS21 to GSK-Biologicals.

CpG ODN 7909 is a synthetic single-stranded phosphorothioateoligodeoxynucleotide (ODN) of 24 bases length. Its base sequence, whichis 5′-TCGTCGTTTTG-TCGTTTTGTCGTT-3′, has been optimized for stimulationof the human immune system. CpG DNA or synthetic ODN containing CpGmotifs are known to activate dendritic cells, monocytes and macrophagesto secrete TH1-like cytokines and to induce TH1 T cell responsesincluding the generation of cytolytic T cells, stimulate NK cells tosecrete IFNg and increase their lytic activity, they also activate Bcells to proliferate (Krieg A et al. 1995 Nature 374: 546, Chu R et al.1997 J. Exp. Med. 186: 1623). CpG 7909 is not antisense to any knownsequence of the human genome. CpG 7909 is a proprietary adjuvantdeveloped by and produced on behalf of Coley Pharmaceutical Group, Inc.,Mass., US.

iNKT Agonists

A subset of T cells known as iNKT (invariant natural killer T) cells aredefined by their expression of a restricted TCR repertoire, consistingof a canonical V-alpha-14-J-alpha-18 or V-alpha-24-J-alpha-18-alphachain in mice and humans respectively. iNKT cells recognize and becomeactivated in response to self or foreign antigenic lipids presented bynon-polymorphic CD1d molecules expressed on the surface of APCs. iNKTcells are activated in response to a variety of infections, and duringinflammatory and autoimmune diseases. iNKT cells provide a means oflinking and coordinating innate and adaptive immune responses, as theirstimulation can induce the downstream activation of DCs, NK cells, B andT cells. It has been demonstrated in vitro that iNKT cells stimulate Bcell proliferation and antibody production.

NKT cells can be activated by alpha-galactosyl-ceramide (alpha-GalCer)or its synthetic analog KRN 7000 (U.S. 2003/0157135). Alpha-GalCer canstimulate NK activity and cytokine production by NKT cells (U.S.2003/0157135). Alpha-GalCer and related glycosylceramides not onlyfunction as antigens, but can also be used as soluble adjuvants capableof enhancing and/or extending the duration of the protective immuneresponses induced by other antigens.

Thus, in some embodiments of the present invention the immunostimulantmay be an iNKT cell agonist. The agonist may be an exogenous orendogenous agonist. It may be a glycosidic agonist (such asalpha-galactasylceramide) or a non-glycosidic agonist (such asthreitolceramide).

Immunostimulatory Lipids or Glycolipids

In some embodiments, the immunostimulant may be a lipid or a glycolipid.Glycolipids presented by CD1 can be grouped into different classesincluding for example diacylglycerolipids, sphingolipids, mycolates andphosphomycoketides (Zajonc and Krenenberg, Current Opinion in StructuralBiology, 2007, 17:521-529). Microbial antigens from pathogenicmycobacteria, such as glucose monomycolates (GMM), mannosylphosphomycoketides and phosphatidylinositol mannosides are known to bepotent ligands for human T cells when presented by group I CD1 molecules(Zajonc an Kronenberg, supra). The immunostimulant can be aglycosylceramide, for example alpha-galactosylceramide (KRN 7000,US2003/0157135) or an analogue thereof, such as for examplethreitolceramide (IMM47) or other non-glycosidic iNKT cell agonists (asdescribed in Silk et al. Cutting Edge J. Immunol, 2008). Furtheranalogues which may be used in accordance with the invention and methodsof producing such analogues are disclosed in WO2007/050668, which isincorporated herein by reference.

TLR Agonists

Intracellular TLRs such as TLRs 3, 7, 8 and 9 recognize nucleic acids.As such, synthetic oligodeoxynucleotides (ODN) such as the TLR9 agonistCpG have previously been used as immunostimulants. These TLRimmunostimulants operate by a different mechanism than that employed bylipids such as alphaGalCer. These immunostimulants directly activate thecell that they are taken up by, culminating in, for example, thesecretion of cytokines and chemokines that result in the furtherstimulation of immune responses.

The TLR expression pattern is specific for each cell type (Chiron et al,2009). TLR expression in human B cells is characterized by highexpression of TLR 1, 6, 7, 9 and 10, with the expression pattern varyingduring B-cell differentiation.

Soluble CpG ODNs are rapidly internalized by immune cells and interactwith TLR9 that is present in endocytic vesicles. Cellular activation bymost members of the TLR family (including TLR9) involves a signalingcascade that proceeds through myeloid differentiation primary responsegene 88 (MYD88), interleukin-1 (IL-1), receptor-activated kinase (IRAK)and tumor-necrosis factor receptor (TNFR)-associated factor 6 (TRAF6),and culminates in the activation of several transcription factors,including nuclear factor-kappaB (NF-kappaB), activating protein 1 (APi),CCAAT-enhancer binding protein (CEBP) and cAMP-responsive elementbinding protein (CREB). These transcription factors directly upregulatecytokine/chemokine gene expression. B cells and plasmacytoid dendriticcells (pDCs) are the main human cell types that express TLR9 and responddirectly to CpG stimulation. Activation of these cells by CpG DNAinitiates an immunostimulatory cascade that culminates in the indirectmaturation, differentiation and proliferation of natural killer (NK)cells, T cells and monocytes/macrophages. Together, these cells secretecytokines and chemokines that create a pro-inflammatory (IL-1-α/β, IL-6,IL-18 and TNF) and T_(H1)-biased (interferon-gamma, IFN-gamma, andIL-12) immune milieu (Klinman, 2004, Nature Reviews, 4:249).

Thus, in some embodiments the immunostimulant is a TRL agonist. Forexample, it is an endosomal TLR agonist, in particular a nucleic acid,such as for example DNA, RNA (either double or single stranded). Theimmunostimulant may, for example comprise a CpG oligodeoxynucleotide ora poly-U nucleic acid.

Saponins

Saponins are taught in: Lacaille-Dubois, M and Wagner H. (1996. A reviewof the biological and pharmacological activities of saponins.Phytomedicine vol 2 pp 363-386). Saponins are steroid or triterpeneglycosides widely distributed in the plant and marine animal kingdoms.

Saponins are known as adjuvants in vaccines for systemic administration.The adjuvant and haemolytic activity of individual saponins has beenextensively studied in the art (Lacaille-Dubois and Wagner, supra). Forexample, Quil A (derived from the bark of the South American treeQuillaja Saponaria Molina), and fractions thereof, are described in U.S.Pat. No. 5,057,540 and “Saponins as vaccine adjuvants”, Kensil, C. R.,Crit Rev Ther Drug Carrier Syst, 1996, 12 (1-2):1-55; and EP 0 362 279B1. Particulate structures, termed Immune Stimulating Complexes(ISCOMS), comprising Quil A or fractions thereof, have been used in themanufacture of vaccines (Morein, B., EP 0 109 942 B1). These structureshave been reported to have adjuvant activity (EP 0 109 942 B1; WO96/11711). The hemolytic saponins QS21 and QS17 (HPLC purified fractionsof Quil A) have been described as potent systemic adjuvants, and themethod of their production is disclosed in U.S. Pat. No. 5,057,540 andEP 0 362 279 B1. Also described in these references is the use of QS7 (anon-haemolytic fraction of Quil-A) which acts as a potent adjuvant forsystemic vaccines. Use of QS21 is further described in Kensil et al.(1991. J. Immunology vol 146, 431-437). Combinations of QS21 andpolysorbate or cyclodextrin are also known (WO 99/10008). Particulateadjuvant systems comprising fractions of QuilA, such as QS21 and QS7 aredescribed in WO 96/33739 and WO 96/11711.

Other saponins which have been used in systemic vaccination studiesinclude those derived from other plant species such as Gypsophila andSaponaria (Bomford et al., Vaccine, 10(9):572-577, 1992).

Cytokines

TH-1 type cytokines, e.g., IFN-gamma, TNF-α, IL-2, IL-12, IL-18, etc,tend to favor the induction of cell mediated immune responses to anadministered antigen. In contrast, high levels of Th2-type cytokines(e.g., IL4, IL-5, IL-6 and IL-10) tend to favor the induction of humoralimmune responses. Interleukin-18 (IL-18), also known as interferon-gamma(IFNg) inducing factor, has been described as an pleotropic cytokinewith immunomodulatory effects that stimulates patient's own immunesystem against disease. IL-18 has several bioactivities, including theability to promote the differentiation of naive CD4 T cells into Th1cells, to stimulate natural killer (NK) cells, natural killer T (NKT)cells, and to induce the proliferation of activated T cells,predominantly cytotoxic T cells (CD8+ phenotype) to secrete gammainterferon (IFN-gamma) (Okamura H. et al. 1998, Adv. Immunol. 70:281-312). IL-18 also mediates Fas-induced tumor death, promotes theproduction of IL-1-α/β and GMCSF, and has anti-angiogenic activity.IFN-α 2a, including pegylated versions thereof (Pegasys), can also beused. Recombinant human Interleukin-7 (r-hIL-7/CYT107) can also be used.

Vaccines

As used herein, “vaccine” includes all prophylactic and therapeuticvaccines.

A vaccine includes an antigen or immunogenic derivative, and anadjuvant. As used herein, the vaccines can be any vaccine that inhibitsany of the viruses described herein, including anti-HIV vaccines whichinhibit HIV through any mechanism.

Where the vaccine is an anti-HIV vaccine, it ideally inhibits or stopsthe HIV virion replication cycle at any one of the following phases ofthe HIV virion cycle:

Phase I. Free State

Phase II. Attachment

Phase III. Penetration

Phase IV. Uncoating

Phase V. Replication

Phase VI. Assembling

Phase VII. Releasing

While many antiviral vaccines use live viruses, with respect to HIVvaccines, it is not advisable to use live viruses, due to the risk ofinfection. However, it is known that deletion of the HIV nef geneattenuates the virus. Desrosiers and his associates have demonstratedthat vaccination of macaques with nef-deleted SIV protected wild-typeSIV challenge (Daniels, M. D. et al. Science 258:1938 (1992);Desrosiers, R. C., et al. Proc. Natl. Acad. Sci. USA 86:6353 (1989)) andothers have demonstrated that nef gene is dispensable for SIV and HIVreplication (Daniels, M. D. et al. Science 258:1938 (1992); Gibbs, J.S., et al. AIDS Res. and Human Retroviruses 10:343 (1994); Igarashi, T.,et al. J. Gen. Virol. 78:985 (1997); Kestler III, H. W., et al. Cell65:651 (1991)). Furthermore, deletion of nef gene renders the virus tobe non-pathogenic in the normally susceptible host (Daniels, M. D. e tal. Science 258:1938 (1992)).

In terms of antigens, subunit vaccines can be used (Cooney E L, et al.,Proc Natl Acad Sci USA 1993; 90; 1882-86; McElrath M J, et al. J InfectDis. 169: 41-47 (1994); Graham B S, et al. J Infect Dis 166: 244-52(1992); and Graham B S, et al. J Infect Dis 167: 533-37 (1993)).HIV-derived antigens include HIV-1 antigen gp120, tat, nef, reversetranscriptase, gag, gp120 and gp160, and various targets in pol Oneexamples of an HIV vaccine is the DermaVir therapeutic HIV vaccine,currently in Phase II clinical studies.

The vaccines of the present invention may additionally contain suitablediluents, adjuvants and/or carriers. In some embodiments, the vaccinescontain an adjuvant which can enhance the immunogenicity of the vaccinein vivo. The adjuvant may be selected from many known adjuvants in theart, including the lipid-A portion of gram negative bacteria endotoxin,trehalose dimycolate of mycobacteria, the phospholipid lysolecithin,dimethyldictadecyl ammonium bromide (DDA), certain linearpolyoxypropylene-polyoxyethylene (POP-POE) block polymers, aluminumhydroxide, and liposomes. The vaccines may also include cytokines thatare known to enhance the immune response including GM-CSF, IL-2, IL-12,TNF-α and IFNγ.

The dose of the vaccine may vary according to factors such as thedisease state, age, sex, and weight of the individual, and the abilityof antibody to elicit a desired response in the individual. Dosageregime may be adjusted to provide the optimum therapeutic response. Forexample, several divided doses may be administered daily or the dose maybe proportionally reduced as indicated by the exigencies of thetherapeutic situation. The dose of the vaccine may also be varied toprovide optimum preventative dose response depending upon thecircumstances.

The vaccines may be administered in a convenient manner such as byinjection (subcutaneous, intravenous, intramuscular, etc.), oraladministration, inhalation, transdermal administration (such as topicalcream or ointment, etc.), or suppository applications.

Recombinant Retrovirus

The recombinant retrovirus of the present invention can be anyretrovirus, including HIV-1, HIV-2, SIV, HTLV-1. Preferably theretrovirus is a human immunodeficiency virus selected from HIV-1 andHIV-2, more preferably, the retrovirus is HIV-1.

The vaccine can be an essentially non-cytolytic retrovirus, wherein theterm “essentially non-cytolytic” means that the retrovirus does notsignificantly damage or kill the cells it infects. In one embodiment,the natural signal sequence of HIV-1 envelope glycoprotein gp120 (NSS)is modified to be essentially non-cytolytic, or is replaced with anessentially non-cytolytic signal sequence.

In one embodiment, the present invention provides an essentiallynon-cytolytic recombinant HIV-1 capable of highly efficient replicationwherein the NSS of the virus' envelope glycoprotein is modifiedsufficiently to prevent cell damage by the virus, preferably byeliminating positively charged amino acids, even more preferably, suchelimination or modification resulting in no more than one (1) andpreferably zero (0) positively charged amino acids. The positivelycharged amino acids which may be modified or replaced include lysine andarginine.

In another embodiment, replacement of the natural signal sequenceresults in a more efficient replication of HIV. Accordingly the presentinvention provides an essentially non-cytolytic recombinant HIV-1capable of highly efficient replication wherein the NSS of the virus'envelope glycoprotein is replaced with an essentially non-cytolytic andmore efficient signal sequence. In a preferred embodiment, replacementof the NSS of the envelope glycoprotein of HIV-1 with either themellitin or IL-3 signal sequence decreases the cytotoxicity of theretrovirus. As such, the present invention includes within its scopereplacement of NSS with any signal sequence which renders the retrovirusessentially non-cytolytic. The inventors have also shown thatreplacement of the NSS with mellitin or IL-3 signal sequences results ina greater level of production and secretion of gp120, in addition to thereduced cytotoxicity. The inventors have also shown that replacement ofthe NSS results in partial deletion the vpu gene. Studies have shown thevpu gene can be completely deleted without any measurable impact on thevirus' ability to replicate (James et al. AIDS Res. Human Retrovirus10:343-350, 1994).

In another embodiment, the retrovirus is rendered avirulent. In apreferred embodiment, the virus is rendered avirulent by deleting thenef gene. Accordingly, the present invention provides an avirulent,essentially non-cytolytic retrovirus which contains a sufficientdeletion of the nef gene to render the virus non-pathogenic and whereinthe virus' envelope glycoprotein gp120 coding sequence is replaced witha more efficient signal sequence. As used herein, “sufficient deletion”means deletion of enough of the sequence to prevent transcription andthereby production of the nef protein product.

In a further embodiment, the retrovirus is rendered avirulent,essentially non-cytolytic, and contains a sufficient deletion of the nefgene and the vpu gene to render the virus non-pathogenic.

Recombinant retroviruses be prepared using techniques known in the art.In one embodiment, the retrovirus can be introduced in a host cell underconditions suitable for the replication and expression of the retrovirusin the host.

The essentially non-cytolytic and avirulent retroviruses can typicallybe produced in large quantities and in a form that is non-pathogenic tothe patient. The viruses can be used, in combination with the JAKinhibitors and, optionally, with HAART, for preventing or treating aretroviral infection. In this use, an effective amount of a killedrecombinant essentially non-cytolytic avirulent retrovirus isadministered to a patient in need of treatment or prophylaxis of aretroviral infection. The term “effective amount” as used herein meansan amount effective and at dosages and for periods of time necessary toachieve the desired result.

In one embodiment, the natural signal sequence of the virus' envelopeglycoprotein, such as gp120, is modified to provide an essentiallynon-cytolytic signal sequence, and/or the virus is rendered avirulent bydeleting the nef gene. In one aspect of this embodiment, themodification to provide a non-cytolytic NSS results in no more than onepositively charged amino acid in the NSS sequence, more preferably zeropositively charged amino acids.

In another aspect of this embodiment, the natural signal sequence of thevirus' envelope glycoprotein, preferably gp120, is replaced with anessentially non-cytolytic signal sequence, and, optionally, the virus isrendered avirulent by deleting the nef gene.

In another aspect of this embodiment, where the NSS is replaced, thenon-cytolytic signal sequence is selected from the group consisting ofthe mellitin sequence and the IL-3 signal sequence.

Chimaeric Antigens

The vaccines can comprise chimaeric antigens, for example, a chimaericinfluenza-HIV vaccine. In one embodiment, the vaccine comprises theA-antigenic loop of influenza haemagglutinin (HA-A), modified toresemble the principle neutralizing determinant (PND) of HIV envelopeglycoprotein gp120. The Chimaeric antigens can be presented as killed orattenuated virus.

Vaccine Production

To produce a vaccine, the antigen is typically combined with apharmaceutically acceptable carrier, and, typically, an adjuvant, tomake a composition comprising a vaccine. This vaccine composition isoptionally combined with an immunostimulant and administered to apatient in need of treatment or prevention of a viral infection.

In one embodiment, the vaccine includes antigens selected for more thanone virus, particularly where co-infection rates are known to be high.One example is HIV and HBV or HCV, or HIV and influenza.

A variety of adjuvants known to one of ordinary skill in the art may beadministered in conjunction with the protein in the vaccine composition.Such adjuvants include, but are not limited to the following: polymers,co-polymers such as polyoxyethylene-polyoxypropylene copolymers,including block co-polymers; polymer P1005; monotide ISA72; Freund'scomplete adjuvant (for animals); Freund's incomplete adjuvant; sorbitanmonooleate; squalene; CRL-8300 adjuvant; alum; QS 21, muramyl dipeptide;trehalose; bacterial extracts, including mycobacterial extracts;detoxified endotoxins; membrane lipids; or combinations thereof.

The vaccine formulations can be presented in unit dosage form, and canbe prepared by conventional pharmaceutical techniques. Such techniquesinclude the step of bringing into association the active ingredient andthe pharmaceutical carrier(s) or excipient(s). In general, theformulations are prepared by uniformly and intimately bringing intoassociation the active ingredient with liquid carriers. Formulationssuitable for parenteral administration include aqueous and non-aqueoussterile injection solutions which may contain anti-oxidants, buffers,bacteriostats and solutes which render the formulation isotonic with theblood of the intended recipient; and aqueous and non-aqueous sterilesuspensions which may include suspending agents and thickening agents.The formulations may be presented in unit-dose or multi-dose containers,for example, sealed ampules and vials, and may be stored in afreeze-dried (lyophilized) condition requiring only the addition of thesterile liquid carrier, for example, water for injections, immediatelyprior to use. Extemporaneous injection solutions and suspensions may beprepared from sterile powders, granules and tablets commonly used by oneof ordinary skill in the art.

Preferred unit dosage formulations are those containing a dose or unit,or an appropriate fraction thereof, of the administered ingredient. Itshould be understood that in addition to the ingredients, particularlymentioned above, the formulations of the present invention may includeother agents commonly used by one of ordinary skill in the art.

The vaccine may be administered through different routes, such as oral,including buccal and sublingual, rectal, parenteral, aerosol, nasal,intramuscular, subcutaneous, intradermal, and topical. The vaccine ofthe present invention may be administered in different forms, includingbut not limited to solutions, emulsions and suspensions, microspheres,particles, microparticles, nanoparticles, and liposomes. It is expectedthat from about 1 to 5 dosages may be required per immunization regimen.Initial injections may range from about 1 mg to 1 gram, with a preferredrange of about 10 mg to 800 mg, and a more preferred range of fromapproximately 25 mg to 500 mg. Booster injections may range from 1 mg to1 gram, with a preferred range of approximately 10 mg to 750 mg, and amore preferred range of about 50 mg to 500 mg.

The volume of administration will vary depending on the route ofadministration. Intramuscular injections may range from about 0.1 ml to1.0 ml.

The vaccines can be administered before, during or after an infection.An infected individual can receive a vaccine directed to the virusinfecting the individual, even though the levels are reduced viatreatment with the TREM-1 inhibitors and/or HAART, stimulating theimmune system to fight the virus that remains in the individual.

The vaccine may be stored at temperatures of from about 4 C to −100 C.The vaccine may also be stored in a lyophilized state at differenttemperatures including room temperature. The vaccine may be sterilizedthrough conventional means known to one of ordinary skill in the art.Such means include, but are not limited to filtration, radiation andheat. The vaccine of the present invention may also be combined withbacteriostatic agents, such as thimerosal, to inhibit bacterial growth.

Those of skill in the art can effectively follow the administration ofthese therapies, and the development of side effects and/or resistantviral strains, without undue experimentation.

The present invention will be better understood with reference to thefollowing non-limiting examples.

Example 1: Representative Screening Procedures for Determining theEffectiveness of a Potential TREM-1 Inhibitor

Compounds can be screened for their ability to inhibit TREM-1, forexample, using the screening methods disclosed in EP 2555789 A1. Thesemethods can be used for antibodies, peptides, aptamers, small molecules,and the like. The methods involve measuring, or qualitatively orquantitatively detecting, the competition of binding of a candidatecompound to the receptor with a labeled competitor (e.g., anantagonist).

In one particular embodiment, the screening method involves:

a) providing a plurality of cells expressing the TREM-1 ligand proteinand cells expressing the TREM-1 protein:

b) incubating these cells with a candidate compound (including proteins,peptides, antibodies, aptamers, and small molecules);

c) determining whether the candidate compound binds to the TREM-1 ligandprotein; and

d) selecting those candidate compounds that inhibit the TREM-1/TREM-1ligand interaction.

An additional screening method involving reactive oxygen species isdescribed in EP 2555789A1. Neutrophils produce reactive oxygen species(“ROS”) in presence of LPS (lipopolysaccharides), anti-TREM-1 mAbs(monoclonal antibodies), or platelets (that constitutively express theTREM-1 ligand) with a synergistic effect of these different inducersthat is mediated by neutrophils membrane-bound TREM-1.

ROS production can be quantified using a fluoregenic substrate (DCFDA:5-(and-6)-carboxy-2′,7′-dichlorodihydro fluorescein diacetate(carboxy-H2DCFDA) *mixed isomers*). For example, 2.5×10⁵ isolated humanneutrophils can be incubated 2 hours at 37° C./5% CO₂ with 5 μM ofDCFDA, in presence of 20 μg/mL anti-TREM-1 mAb with or without 100 ng/mLLPS. ROS production by TREM-1 activation and its modulations bypolypeptides can then be quantified by flow cytometry. If the studiedpeptide inhibits TREM-1, mean fluorescence intensity (MFI) decrease ascompared to conditions without TREM-1 mAb. This rapid assay allows oneto quickly determine which are the most active peptides at inhibitingTREM-1. In general, such screening methods involve providing appropriatecells which express the TREM-1 protein, or its orthologs or derivativesthereof, on their surface.

In one aspect of this embodiment, a nucleic acid encoding the TREM-1protein can be used to transfect cells to express the TREM-1 protein.Such a transfection can be achieved by methods well known in the art.

Example 2: Comparison of TREM-1 Inhibitors to ConventionalAntiretroviral Therapy

Current first line highly active antiretroviral therapy (HAART) for thetreatment of human immunodeficiency virus (HIV-1) infections combinestwo nucleoside reverse transcriptase inhibitors (NRTI) together witheither a protease inhibitor (PI) or non-nucleoside reverse transcriptaseinhibitor (NNRTI). These drug combinations have markedly decreasedmortality and morbidity from HIV-1 infections in the developed world.

Existing therapies cannot eradicate HIV-1 infection because of thecompartmentalization of the virus and its latent properties. Therefore,chronic therapy remains the standard of care for the foreseeable future.Although HAART regimens are selected in part to minimize crossresistance, and thereby delay the emergence of resistant viruses, allregimens eventually fail, due primarily to lack of adherence to strictregimens, delayed toxicities and/or the emergence of drug-resistantHIV-1 strains, making it a major imperative to develop regimens thatdelay, prevent or attenuate the onset of resistance for second linetreatments for infected individuals who have already demonstratedmutations. The occurrence of common resistance mutations, includingthymidine analog mutations (TAM), K65R and M184V, need to be a continuedfocus in the rational design of HIV-1 NRTI drug development.

The objectives of this study were to evaluate TREM-1 inhibitors that donot appear to function in the same manner as NRTI, NNRTI, proteaseinhibitors, entry inhibitors, integrase inhibitors, and the like. Inthis example, TREM-1 inhibitors were combined with JAK inhibitors, suchas Jakafi (Incyte) and Tofacitinib (Pfizer).

PBM Cell and M

Protocol for Antiviral Potency

Macrophages can be isolated as follows: Monocytes can be isolated frombuffy coats of HIV-1 negative, HBV/HCV-negative donors with densitygradient centrifugation coupled with enrichment for CD14+ monocytes withRosette Sep antibody cocktail (Stem Cell Technologies, Vancouver,British Columbia). Cells can be seeded at a concentration of 1.0×10⁶cells/well for 1 hr at 37° C. and 5% CO₂ to confer plastic adherenceprior to repeated washes with 1×PBS. Macrophages can be maintained inmedium containing 100 U/ml macrophage colony-stimulating factor (m-CSF,R&D Systems, Minneapolis, Minn.), supplemented with 20% fetal calf serum(Atlanta Biologicals, Lawrenceville, Ga.) and 1%penicillin/streptomyocin (Invitrogen, Carlsbad, Calif.) for 7 days (37°C., 5% CO₂) prior to testing.

Macrophage infections: Macrophages can be cultured as described abovefor 7 days. For acute infection, macrophages can be serum starved for 8hrs prior to infection and cultured for 2 hr in medium containingvarious concentrations of AZT (positive control) or Tofacitinib orJakafi for 2 hr prior to removal of drug-containing medium and 4 hrinfection with HIV-1_(BaL) at 0.1 MOI in the absence of drug. Four hrafter infection, virus can be removed and drug-containing mediumreturned to the cultures. Supernatants can be collected on day 7post-infection and HIV-1 p24 can be quantified via ELISA (ZeptometrixCorporation, Buffalo, N.Y.). EC₅₀ analysis can be performed usingCalcuSyn software (BioSoft Corporation, Cambridge, UK).

FIG. 1 shows that extracellular TNF-α production is significantlyincreased in HIV-infected primary human macrophages. Primary humanmacrophages were exposed to 5 μg/ml LPS (positive control) or acuteHIV-1 infection in resting or activated macrophages (absence or presenceof constitutive 5 ng/ml GM-CSF). Acute HIV-1 infection significantlyincreases TNF-α production in both resting and activated macrophages(blue and brown bars) versus uninfected controls (right panels) (p<0.01,student's t-test). All time points were assessed at 48 hours post virusor LPS exposure. Data are mean and standard deviation from three donorsperformed in replicates. * indicates significant increase versusuninfected controls.

Human PBM cells can be isolated as follows: Lymphocytes can be isolatedfrom buffy coats derived from healthy donors. Activated lymphocytes canbe maintained for 72 hr in medium supplemented with 6 μg/mlphytohemagglutinin (PHA) (Cape Cod associates, East Falmouth, Mass.).Media can be comprised of RPMI media supplemented with 20% fetal calfserum, 1% penicillin/streptomyocin and 2% L-glutamine (Sigma Aldrich,San Jose, Calif.).

Human PBM cell infections: Testing can be performed in duplicate with atleast 3 independent assays. Cells can be incubated in RPMI medium(HyClone, Logan, Utah) containing HR-IL2 (26.5 units/ml) and 20% fetalcalf serum. Infections can be performed by adding HIV-1_(LAI) followedby a further incubation at 37° C., 5% CO2, 1 hr prior to addition ofdrugs. Assays can be performed in 24 well plates (BD Biosciences,Franklin Lakes, N.J.). One ml of supernatant can be collected after 5days in culture and then centrifuged at 12,000 rpm for 2 hr at 4° C. ina Jouan Br43i (Thermo Electron Corp., Marietta, Ohio). The product ofthe RT assay can be quantified using a Packard harvester and direct betacounter and the data can be analyzed as previously described (Schinaziet al., 1990).

Cytotoxicity Assay

The toxicity of the compounds was assessed in Vero, human PBM, CEM(human lymphoblastoid), as described previously (see Schinazi R. F.,Sommadossi J.-P., Saalmann V., Cannon D. L., Xie M.-Y., Hart G. C.,Smith G. A. & Hahn E. F. Antimicrob. Agents Chemother. 1990, 34,1061-67), and also in MØ cells. Cycloheximide was included as positivecytotoxic control, and untreated cells exposed to cell culture mediumwere included as negative controls.

The cytotoxicity IC₅₀ was obtained from the concentration-response curveusing the median effective method described previously (see Chou T.-C. &Talalay P. Adv. Enzyme Regul. 1984, 22, 27-55; Belen'kii M. S. &Schinazi R. F. Antiviral Res. 1994, 25, 1-11).

The potency and toxicity of JAK inhibitors Tofacitinib and Jakafi versusFDA approved controls AZT and 3TC was evaluated in acutely infectedactivated MØ, as well as in PBM cells. The EC₅₀ data (μM) is shown inFIG. 2. Also shown in FIG. 2 are the IC₅₀ values (μM) for thesecompounds in PBM, MØ cells, CEM cells, and Vero cells.

Primary human macrophages were exposed to 5 μg/ml LPS (positive control)or acute HIV-1 infection in resting or activated macrophages (absence orpresence of constitutive 5 ng/ml GM-CSF). Acute HIV-1 infectionsignificantly increases TNF-α production in both resting and activatedmacrophages (blue and brown bars) versus uninfected controls (rightpanels) (p<0.01, student's t-test). All time points were assessed at 48hours post virus or LPS exposure. Data are mean and standard deviationfrom three donors performed in replicates.

The data show a very large therapeutic window (ratio oftoxicity/potency), and that the JAK inhibitor compounds havesubstantially the same EC₅₀ and substantially lower IC₅₀ values thanAZT.

Cell proliferation was evaluated in activated PBM cells incubated for 5days with various concentrations of Tofacitinib and Jakafi, withcycloheximide as a positive control, and a “cells plus media” controlused as well. The data is shown in FIG. 2, in terms of total cell number(10⁶ cells) versus M drug in medium. The data shows that Tofacitinib andJakafi do not affect total cell proliferation at antiviralconcentrations.

Cell viability was evaluated in activated PBM cells incubated for 5 dayswith various concentrations of Tofacitinib and Jakafi, withcycloheximide as a positive control, and a “cells plus media” controlused as well.

FIGS. 3A and 3B show the antiviral potency for co-administration ofruxolitinib and tofacitinib in primary human lymphocytes (FIG. 3A) andmacrophages (FIG. 3B, in terms of cell viability (%) versus M drug inmedium.

Co-treatment of ruxolitinib and tofacitinib (dotted line) at a ratio of1:4 (lymphocytes, FIG. 3A) or 1:1 (macrophages, FIG. 3B) demonstratedsynergistic antiviral potency as calculated by CalcuSyn (Biosoft, Inc.,Cambridge, Great Britain). Triangles, tofacitinib alone; squares,Ruxolitinib alone; dotted line with circles, ruxolitinib+tofacitinib.Data are mean and standard deviations for at least three independentexperiments conducted with at least 4 pooled donors, and duplicateswithin each experiment. Numerical values on left Y axes representpercent inhibition versus no drug control. Numerical values on right Yaxes represent cpm⁻¹/μl (RT values) or pg⁻¹/ml p24 for PBM cells andmacrophages, respectively.

The data also show that Tofacitinib and Jakafi do not affect total cellviability at antiviral concentrations. The effect of Jak inhibitors onthe proliferation and viability of PHA or PHA+IL-2 stimulated primaryhuman lymphocytes is shown in FIGS. 4A-D. For PHA stimulatedlymphocytes, viability and proliferation were not significantlydifferent than that of cells exposed to media alone for allconcentrations of either ruxolitinib or tofacitinib (FIG. 4A, FIG. 4C).For PHA+IL-2 stimulated lymphocytes, viability was not significantlydifferent than that of cells exposed to media alone for allconcentrations of either ruxolitinib (dotted line with squares) ortofacitinib (light gray line with diamonds) (FIG. 4B), howeverproliferation was significantly inhibited by 1 μM of ruxolitinib ortofacitinib (FIG. 4D). For all experiments, cells were incubated withmedia alone or drug-containing medium for 5 days prior to assessment ofcell count and viability. The positive control of cycloheximide (solidline, diamonds) was toxic in a dose dependent manner as expected. Dataare mean and standard deviations for at least three independentexperiments conducted with at least four pooled donors, and duplicateswithin each experiment. Dotted bar represents mean cell count orviability for cells maintained in drug-free medium.

The TREM-1 Peptide Significantly Reduces HIV-Induced MonocyteActivation.

Primary human monocytes were exposed to replication competent M-R5 HIV-1BaL for 5 days prior to quantification of HIV-induced activation(CD14+/CD16⁺ monocytes; tandem two color FACS). Data is shown in FIGS.5A and 5B. FIG. 5A shows that HIV infection is associated with anincrease in the number of activated monocytes. FIG. 5B shows thatfollowing administration of TREM-1 peptide, the number of activatedmonocytes was lower.

Assay represents three independent donors conducted with duplicates.Data are mean and standard deviations, * indicates significant reductionversus BaL infected, no drug control (one-way ANOVA).

TREM-1 peptide significantly reduced HIV-induced activation in primaryhuman macrophages without altering CD4 expression. Primary humanmacrophages were treated with replication competent M-R5 HIV-1 BaL for 5days in the presence or absence of various concentrations of TREM-1peptide. TREM-1 peptide significantly reduces HIV-1 induced activationmarkers HLA-DR (FIG. 6A), CCR5 (FIG. 6B), and CD163 (FIG. 6C); * one wayANOVA). TREM-1 peptide does not reduce CD4 expression (FIG. 6D),demonstrating that CD4 receptor expression-mediated innate and adaptiveimmunity is not altered. HIV-1 BaL significantly increases activationmarkers CD163, CCR5, and CD163 versus no virus control (**; one-wayANOVA). Data are mean and standard deviation for three independentdonors conducted in duplicates.

These assays can be repeated with the TREM-1 inhibitors describedherein.

CONCLUSION

In conclusion, Tofacitinib and Jakafi are potent, sub-micromolarinhibitors of HIV-1 replication in both PBM cells and MØ cells. Thecompounds do not affect viability or proliferation for PBM cells and MØcells, or total cell number, up to around 10 μM (2-3 logs above EC₅₀).The therapeutic window (ratio of toxicity:potency) is wide for both celltypes (24->100).

Example 3: Mitochondrial Toxicity Assays in HepG2 Cells

i) Effect of the TREM-1 Inhibitors Described Herein on Cell Growth andLactic Acid Production:

The effect on the growth of HepG2 cells can be determined by incubatingcells in the presence of 0 μM, 0.1 μM, 1 μM, 10 μM and 100 μM drug.Cells (5×10⁴ per well) were plated into 12-well cell culture clusters inminimum essential medium with nonessential amino acids supplemented with10% fetal bovine serum, 1% sodium pyruvate, and 1%penicillin/streptomycin and incubated for 4 days at 37° C. At the end ofthe incubation period the cell number was determined using ahemocytometer. Also taught by Pan-Zhou X-R, Cui L, Zhou X-J, SommadossiJ-P, Darley-Usmer V M. “Differential effects of antiretroviralnucleoside analogs on mitochondrial function in HepG2 cells” Antimicrob.Agents Chemother. 2000; 44: 496-503. To measure the effects of thecompounds on lactic acid production, HepG2 cells from a stock culturecan be diluted and plated in 12-well culture plates at 2.5×10⁴ cells perwell. Various concentrations (0 μM, 0.1 μM, 1 μM, 10 μM and 100 μM) ofthe compounds can be added, and the cultures incubated at 37° C. in ahumidified 5% CO₂ atmosphere for 4 days. At day 4 the number of cells ineach well can be determined and the culture medium collected. Theculture medium was filtered, and the lactic acid content in the mediumdetermined using a colorimetric lactic acid assay (Sigma-Aldrich). Sincelactic acid product can be considered a marker for impairedmitochondrial function, elevated levels of lactic acid productiondetected in cells grown in the presence of the compounds would indicatea drug-induced cytotoxic effect.

ii) Effect on the Compounds on Mitochondrial DNA Synthesis:

a real-time PCR assay to accurately quantify mitochondrial DNA contenthas been developed (see Stuyver L J, Lostia S, Adams M, Mathew J S, PaiB S, Grier J, Tharnish P M, Choi Y, Chong Y, Choo H, Chu C K, Otto M J,Schinazi R F. Antiviral activities and cellular toxicities of modified2′,3′-dideoxy-2′,3′-didehydrocytidine analogs. Antimicrob. AgentsChemother. 2002; 46: 3854-60). This assay can be used to determine theeffect of the compounds on mitochondrial DNA content. In this assay,low-passage-number HepG2 cells are seeded at 5,000 cells/well incollagen-coated 96-well plates. The compounds are added to the medium toobtain final concentrations of 0 μM, 0.1 μM, 10 μM and 100 μM. Onculture day 7, cellular nucleic acids are prepared by using commerciallyavailable columns (RNeasy 96 kit; Qiagen). These kits co-purify RNA andDNA, and hence, total nucleic acids were eluted from the columns. Themitochondrial cytochrome c oxidase subunit II (COXII) gene and the8-actin or rRNA gene were amplified from 5 μl of the eluted nucleicacids using a multiplex Q-PCR protocol with suitable primers and probesfor both target and reference amplifications. For COXII the followingsense, probe and antisense primers are used, respectively:5′-TGCCCGCCATCATCCTA-3′ (SEQ ID NO. 8),5′-tetrachloro-6-carboxyfluorescein-TCCTCATCGCCCTCCCATCCC-TAMRA-3′ (SEQID NO. 9) and 5′-CGTCTGTTATGTAAAGGATGCGT-3′ (SEQ ID NO. 10). For exon 3of the 8-actin gene (GenBank accession number E01094) the sense, probe,and antisense primers are 5′-GCGCGGCTACAGCTTCA-3′ (SEQ ID NO. 11),5′-6-FAMCACCACGGCCGAGCGGGATAMRA-3′ (SEQ ID NO. 12) and5′-TCTCCTTAATGTCACGCACGAT-3′ (SEQ ID NO. 13), respectively. The primersand probes for the rRNA gene are commercially available from AppliedBiosystems. Since equal amplification efficiencies are obtained for allgenes, the comparative CT method can be used to investigate potentialinhibition of mitochondrial DNA synthesis. The comparative CT methoduses arithmetic formulas in which the amount of target (COXII gene) isnormalized to the amount of an endogenous reference (the β-actin or rRNAgene) and is relative to a calibrator (a control with no drug at day 7).The arithmetic formula for this approach is given by 2-ΔΔCT, where ΔΔCTis (CT for average target test sample−CT for target control)−(CT foraverage reference test−CT for reference control) (see Johnson M R, KWang, J B Smith, M J Heslin, R B Diasio. Quantitation ofdihydropyrimidine dehydrogenase expression by real-time reversetranscription polymerase chain reaction. Anal. Biochem. 2000;278:175-184). A decrease in mitochondrial DNA content in cells grown inthe presence of drug would indicate mitochondrial toxicity.

iii) Electron Microscopic Morphologic Evaluation:

NRTI induced toxicity has been shown to cause morphological changes inmitochondria (e.g., loss of cristae, matrix dissolution and swelling,and lipid droplet formation) that can be observed with ultrastructuralanalysis using transmission electron microscopy (see Cui L, Schinazi RF, Gosselin G, Imbach J L. Chu C K, Rando R F, Revankar G R, SommadossiJ P. Effect of enantiomeric and racemic nucleoside analogs onmitochondrial functions in HepG2 cells. Biochem. Pharmacol. 1996, 52,1577-1584; Lewis W, Levine E S, Griniuviene B, Tankersley K O, ColacinoJ M, Sommadossi J P, Watanabe K A, Perrino F W. Fialuridine and itsmetabolites inhibit DNA polymerase gamma at sites of multiple adjacentanalog incorporation, decrease mtDNA abundance, and cause mitochondrialstructural defects in cultured hepatoblasts. Proc Natl Acad Sci USA.1996; 93: 3592-7; Pan-Zhou X R, L Cui, X J Zhou, JP Sommadossi, V MDarley-Usmar. Differential effects of antiretroviral nucleoside analogson mitochondrial function in HepG2 cells. Antimicrob. Agents Chemother.2000, 44, 496-503). For example, electron micrographs of HepG2 cellsincubated with 10 μM fialuridine (FIAU;1,2′-deoxy-2′-fluoro-1-D-arabinofuranosly-5-iodo-uracil) showed thepresence of enlarged mitochondria with morphological changes consistentwith mitochondrial dysfunction. To determine if the JAK inhibitorcompounds promote morphological changes in mitochondria, HepG2 cells(2.5×10⁴ cells/mL) can be seeded into tissue cultures dishes (35 by 10mm) in the presence of 0 μM, 0.1 μM, 1 μM, 10 μM and 100 μM nucleosideanalog. At day 8, the cells can be fixed, dehydrated, and embedded inEponas described previously. Thin sections can be prepared, stained withuranyl acetate and lead citrate, and then examined using transmissionelectron microscopy.

Example 4: Mitochondrial Toxicity Assays in Neuro2A Cells

To estimate the potential of the TREM-1 inhibitor compounds to causeneuronal toxicity, mouse Neuro2A cells (American Type Culture Collection131) can be used as a model system (see Ray A S, Hernandez-Santiago B I,Mathew J S, Murakami E, Bozeman C, Xie M Y, Dutschman G E, Gullen E,Yang Z, Hurwitz S, Cheng Y C, Chu C K, McClure H, Schinazi R F, AndersonK S. Mechanism of anti-human immunodeficiency virus activity ofbeta-D-6-cyclopropylamino-2′,3′-didehydro-2′,3′-dideoxyguanosine.Antimicrob. Agents Chemother. 2005, 49, 1994-2001). The concentrationsnecessary to inhibit cell growth by 50% (CC₅₀) can be measured using the3-(4,5-dimethyl-thiazol-2-yl)-2,5-diphenyltetrazolium bromide dye-basedassay, as described. Perturbations in cellular lactic acid andmitochondrial DNA levels at defined concentrations of drug can becarried out as described above.

Example 5: Assay for Bone Marrow Cytotoxicity

Primary human bone marrow mononuclear cells can be obtained commerciallyfrom Cambrex Bioscience (Walkersville, Md.). CFU-GM assays can becarried out using a bilayer soft agar in the presence of 50 units/mLhuman recombinant granulocyte/macrophage colony-stimulating factor,while BFU-E assays used a methylcellulose matrix containing 1 unit/mLerythropoietin (see Sommadossi J P, Carlisle R. Toxicity of3′-azido-3′-deoxythymidine and 9-(1,3-dihydroxy-2-propoxymethyl) guaninefor normal human hepatopoietic progenitor cells in vitro. Antimicrob.Agents Chemother. 1987; 31: 452-454; Sommadossi, JP, Schinazi, RF, Chu,C K, and Xie, MY. Comparison of Cytotoxicity of the (−) and (+)enantiomer of 2′,3′-dideoxy-3′-thiacytidine in normal human bone marrowprogenitor cells. Biochem. Pharmacol. 1992; 44:1921-1925). Eachexperiment can be performed in duplicate in cells from three differentdonors. AZT can be used as a positive control. Cells can be incubated inthe presence of a TREM-1 inhibitor compound for 14-18 days at 37° C.with 5% CO₂, and colonies of greater than 50 cells can be counted usingan inverted microscope to determine IC₅₀. The 50% inhibitoryconcentration (IC₅₀) can be obtained by least-squares linear regressionanalysis of the logarithm of drug concentration versus BFU-E survivalfractions. Statistical analysis can be performed with Student's t testfor independent non-paired samples.

Example 6: Cytotoxicity Assay

The toxicity of the compounds can be assessed in Vero, human PBM, CEM(human lymphoblastoid), MT-2, and HepG2 cells, as described previously(see Schinazi R. F., Sommadossi J.-P., Saalmann V., Cannon D. L., XieM.-Y., Hart G. C., Smith G. A. & Hahn E. F. Antimicrob. AgentsChemother. 1990, 34, 1061-67). Cycloheximide can be included as positivecytotoxic control, and untreated cells exposed to solvent can beincluded as negative controls. The cytotoxicity IC₅₀ can be obtainedfrom the concentration-response curve using the median effective methoddescribed previously (see Chou T.-C. & Talalay P. Adv. Enzyme Regul.1984, 22, 27-55; Belen'kii M. S. & Schinazi R. F. Antiviral Res. 1994,25, 1-11).

Example 7: Bioavailability Assay in Cynomolgus Monkeys

The following procedure can be used to determine whether the compoundsare bioavailable. Within 1 week prior to the study initiation, acynomolgus monkey can be surgically implanted with a chronic venouscatheter and subcutaneous venous access port (VAP) to facilitate bloodcollection and can undergo a physical examination including hematologyand serum chemistry evaluations and the body weight recording. Eachmonkey (six total) receives approximately 250 μCi of ³H activity witheach dose of active compound at a dose level of 10 mg/kg at a doseconcentration of 5 mg/mL, either via an intravenous bolus (3 monkeys,IV), or via oral gavage (3 monkeys, PO). Each dosing syringe is weighedbefore dosing to gravimetrically determine the quantity of formulationadministered. Urine samples are collected via pan catch at thedesignated intervals (approximately 18-0 hours pre-dose, 0-4, 4-8 and8-12 hours post-dosage) and processed. Blood samples are collected aswell (pre-dose, 0.25, 0.5, 1, 2, 3, 6, 8, 12 and 24 hours post-dosage)via the chronic venous catheter and VAP or from a peripheral vessel ifthe chronic venous catheter procedure should not be possible. The bloodand urine samples are analyzed for the maximum concentration (Cmax),time when the maximum concentration is achieved (TmaX), area under thecurve (AUC), half life of the dosage concentration (TV), clearance (CL),steady state volume and distribution (Vss) and bioavailability (F).

Example 8: Cell Protection Assay (CPA)

The assay can be performed essentially as described by Baginski, S. G.;Pevear, D. C.; Seipel, M.; Sun, S. C. C.; Benetatos, C. A.; Chunduru, S.K.; Rice, C. M. and M. S. Collett “Mechanism of action of a pestivirusantiviral compound” PNAS USA 2000, 97 (14), 7981-7986. MDBK cells (ATCC)are seeded onto 96-well culture plates (4,000 cells per well) 24 hoursbefore use. After infection with BVDV (strain NADL, ATCC) at amultiplicity of infection (MOI) of 0.02 plaque forming units (PFU) percell, serial dilutions of test compounds are added to both infected anduninfected cells in a final concentration of 0.5% DMSO in growth medium.Each dilution is tested in quadruplicate.

Cell densities and virus inocula are adjusted to ensure continuous cellgrowth throughout the experiment and to achieve more than 90%virus-induced cell destruction in the untreated controls after four dayspost-infection. After four days, plates are fixed with 50% TCA andstained with sulforhodamine B. The optical density of the wells is readin a microplate reader at 550 nm.

The 50% effective concentration (EC₅₀) values are defined as thecompound concentration that achieved 50% reduction of cytopathic effectof the virus.

Example 9: Plaque Reduction Assay

For a compound, the effective concentration is determined in duplicate24-well plates by plaque reduction assays. Cell monolayers are infectedwith 100 PFU/well of virus. Then, serial dilutions of test compounds inMEM supplemented with 2% inactivated serum and 0.75% of methyl celluloseare added to the monolayers. Cultures are further incubated at 37° C.for 3 days, then fixed with 50% ethanol and 0.8% Crystal Violet, washedand air-dried. Then plaques are counted to determine the concentrationto obtain 90% virus suppression.

Example 10: Yield Reduction Assay

For a compound, the concentration to obtain a 6-log reduction in viralload is determined in duplicate 24-well plates by yield reductionassays. The assay is performed as described by Baginski, S. G.; Pevear,D. C.; Seipel, M.; Sun, S. C. C.; Benetatos, C. A.; Chunduru, S. K.;Rice, C. M. and M. S. Collett “Mechanism of action of a pestivirusantiviral compound” PNAS USA 2000, 97 (14), 7981-7986, with minormodifications.

Briefly, MDBK cells are seeded onto 24-well plates (2×10⁵ cells perwell) 24 hours before infection with BVDV (NADL strain) at amultiplicity of infection (MOI) of 0.1 PFU per cell. Serial dilutions oftest compounds are added to cells in a final concentration of 0.5% DMSOin growth medium. Each dilution is tested in triplicate. After threedays, cell cultures (cell monolayers and supernatants) are lysed bythree freeze-thaw cycles, and virus yield is quantified by plaque assay.Briefly, MDBK cells are seeded onto 6-well plates (5×10⁵ cells per well)24 h before use. Cells are inoculated with 0.2 mL of test lysates for 1hour, washed and overlaid with 0.5% agarose in growth medium. After 3days, cell monolayers are fixed with 3.5% formaldehyde and stained with1% crystal violet (w/v in 50% ethanol) to visualize plaques. The plaquesare counted to determine the concentration to obtain a 6-log reductionin viral load.

Example 11: Assay for Effectiveness Against Dengue

One representative high throughput assay for identifying compoundsuseful for treating Dengue is described in Lim et al., A scintillationproximity assay for dengue virus NS5 2′-O-methyltransferase-kinetic andinhibition analyses, Antiviral Research, Volume 80, Issue 3, December2008, Pages 360-369.

Dengue virus (DENV) NS5 possesses methyltransferase (MTase) activity atits N-terminal amino acid sequence and is responsible for formation of atype 1 cap structure, m7GpppAm2′-O in the viral genomic RNA. Optimal invitro conditions for DENV2 2′-O-MTase activity can be characterizedusing purified recombinant protein and a short biotinylated GTP-cappedRNA template. Steady-state kinetics parameters derived from initialvelocities can be used to establish a robust scintillation proximityassay for compound testing. Pre-incubation studies by Lim et al.,Antiviral Research, Volume 80, Issue 3, December 2008, Pages 360-369,showed that MTase-AdoMet and MTase-RNA complexes were equallycatalytically competent and the enzyme supports a random bi bi kineticmechanism. Lim validated the assay with competitive inhibitory agents,S-adenosyl-homocysteine and two homologues, sinefungin anddehydrosinefungin. A GTP-binding pocket present at the N-terminal ofDENV2 MTase was previously postulated to be the cap-binding site. Thisassay allows rapid and highly sensitive detection of 2′-O-MTase activityand can be readily adapted for high-throughput screening for inhibitorycompounds. It is suitable for determination of enzymatic activities of awide variety of RNA capping MTases.

Example 12: Evaluation of Antiviral Activity Against Chikungunya

One representative assay for identifying therapies useful for treatingthe Chikungunya virus is described in Couderc T, et al, PLoS Pathogens,A Mouse Model for Chikungunya: Young Age and Inefficient Type-IInterferon Signaling Are Risk Factors for Severe Disease, 2008 Feb. 8;4(2):e29. In this assay, the effect of TREM-1 inhibitors, alone or incombination, can be assessed. Live, replication competent Chikungunyavirus is used to confer systemic infection in the murine model, whereininfection is in monocytes, macrophages and other permissive cell types.In the presence of TREM-1 inhibitors, alone or in combination, and theirimpact on Chikungunya virus-driven inflammation, activation, conferenceof rheumatoid arthritis and other systemic effects, can be quantified.Cellular events such as Chikungunya virus-induced monocyte/macrophageactivation, systemic inflammation including IL-6, TNF-α, IL-1α/β, orother cytokine levels, can be quantified.

Another assay which can be used to measure the effect of TREM-1inhibitors on Chikungunya infection, alone or in combination, is aprimary human or murine macrophages, also described by the abovereference above. Human or murine macrophages can be infected in vitro orex vivo and measures of secreted inflammatory cytokines such as IL-6,TNF-α, IL-1α/β, or GM-CSF can be quantified in supernatants as candown-regulation of TREM-1 inhibitor-induced activation markers such assCD163, HLA-DR, CD163, or IL-6R.

There are now many replicon systems available for Dengue and Chikungunyain the literature. Examples include those disclosed in PCT WO2008030220and Glasker et al., “Virus replicon particle based Chikungunya virusneutralization assay using Gaussia luciferase as readout,” VirologyJournal 2013, 10:235. Glasker discloses that Chikungunya virus (CHIKV)has been responsible for large epidemic outbreaks causing fever,headache, rash and severe arthralgia. As nucleic acid amplification canonly be used during the viremic phase of the disease, serological testslike neutralization assays are necessary for CHIKV diagnosis and fordetermination of the immune status of a patient. Furthermore,neutralization assays represent a useful tool to validate the efficacyof potential vaccines. As CHIKV is a BSL3 agent, neutralization assayswith infectious virus need to be performed under BSL3 conditions. Thefollowing is a neutralization assay based on non-infectious virusreplicon particles (VRPs).

Methods:

VRPs can be produced by co-transfecting baby hamster kidney-21 cellswith a CHIKV replicon expressing Gaussia luciferase (Gluc) and twohelper RNAs expressing the CHIKV capsid protein or the remainingstructural proteins, respectively. The resulting single round infectiousparticles can be used in CHIKV neutralization assays using secreted Glucas readout.

Results:

Upon co-transfection of a CHIKV replicon expressing Gluc and the helperRNAs, VRPs can be be produced efficiently under optimized conditions at32° C. Infection with VRPs can be be measured via Gluc secreted into thesupernatant. The successful use of VRPs in CHIKV neutralization assayscan be demonstrated using a CHIKV neutralizing monoclonal antibody orsera from CHIKV infected patients. In the 96-well format, a highmultiplicity of infection is favored, while in the 24-well formatreliable results are also obtained using lower infection rates.

Evaluation of the neutralization assay is already possible at the sameday of infection.

Conclusions:

The VRP based CHIKV neutralization assay using Gluc as readoutrepresents a fast and useful method to determine CHIKV neutralizingantibodies without the need of using infectious CHIKV.

Example 13: Extrapolation of the Data from Example 2 Relative to a Curefor HIV, as Well as Other Viruses

The data shown in FIGS. 5A-B and 6A-D demonstrate that blockade ofTREM-1 at the receptor level results in potent inhibition of viralreplication and virally-induced activation. These data demonstrate thatTREM-1 inhibition represents a novel, potent mechanism to inhibit viralreplication in cells expressing TREM-1. Inhibition of viral replicationwith the TREM-1 inhibitor represents a proof of principle whereininhibition of this receptor down-regulates the cellular activation thatis critical to allow for the virus to replicate in these cells. Thismechanism, which has been reduced to practice with HIV, is alsoapplicable to other viruses that infected cells expressing TREM-1, orinteract with cells expressing TREM-1, including but not limited toChikungunya, West Nile, Dengue, Influenza, and other viruses. These dataalso demonstrate that virus-induced activation allows for the virus toreplicate in TREM-1 expressing cells, and that inhibition ofvirus-induced activation prevents the virus from replicating. Thisapplication also applies to other viruses that rely on cellularactivation to replicate in host cells, including but not limited toChikungunya, West Nile, Dengue, Influenza, and other viruses.

To demonstrate this, primary human macrophages were infected with anM-R5 replication competent HIV-1 (BaL) in the presence of variousconcentrations of AZT (control) or TREM-1 peptide. Extracellular viruswas quantified 7 days after infection (HIV-1 p24 ELISA). The TREM-1peptide demonstrates nanomolar inhibition of HIV-1 replication inprimary human macrophages. As expected, AZT control demonstratednanomolar inhibition of viral replication. The TREM-1 peptide did notdemonstrate any apparent toxicity (quantified by zombie violet live/deaddye, Violet channel, FACS). The TREM-1 peptide did not demonstrateantiviral potency up to 50 μM in primary human peripheral bloodmononuclear (PBM) cells (data not shown). The data is shown below inTable 2.

TABLE 2 Antiviral potency of the TREM-1 peptide in primary humanmacrophages. Antiviral Antiviral potency in potency in Toxicity inprimary primary primary human human human macrophages macrophagesmacrophages Therapeutic Drug Class (EC₅₀, μM) (EC₉₀, μM) (IC₅₀, μM)index TREM-1 TREM-1 0.14 3.4 >100 >100 peptide inhibitor ≤0.01 (43.1)7.6 >100 <0.01 (73.6) 6.4 0.15 0.10 AZT Nucleoside 0.01 ± 0.02 0.7 ±0.2 >100 >100 analog

While the foregoing specification teaches the principles of the presentinvention, with examples provided for the purpose of illustration, itwill be understood that the practice of the invention encompasses all ofthe usual variations, adaptations and/or modifications as come withinthe scope of the following claims and their equivalents. All referencescited herein are incorporated by reference in their entirety for allpurposes.

1. A method for treating an HIV infection, comprising administering to a patient in need thereof an effective antiviral amount of a TREM-1 inhibitor.
 2. The method of claim 1, wherein the TREM-1 inhibitor is selected from the group consisting of TLT-1, -CDR2 (SAVDRRAPAGRR, SEQ ID NO 1), TLT-1-CDR3 (CMVDGARGPQILHR, SEQ ID NO 2), LR17 (LQEEDAGEYGCMVDGAR, SEQ ID NO 3), LR6-1 (LQEEDA, SEQ ID NO 4), LR6-2 (EDAGEY, SEQ ID NO 5), LR6-3 (GEYGCM, SEQ ID NO 6), LR12 (LQEEDAGEYGCM, SEQ ID NO 7), prodrugs thereof, conjugated versions thereof, deuterated variations thereof, analogs thereof comprising non-naturally occurring amino-acids, functional variations thereof including a different sequence of amino acids but which retain TREM-1 inhibitory activity, analogs thereof in which each amino acid can be, individually, a D or L isomer, and combinations of L-isoforms with D-isoforms thereof, wherein the peptides can optionally be stabilized by micelles.
 3. The method of claim 1, wherein the TREM-1 inhibitor is selected from the group consisting of MicroRNA 294, human cathelicidin LL-37, the F-c portion of human IgG (AdTREM-1Ig), antibodies directed to the TREM-1 and/or sTREM-1 or TREM-1 and/or sTREM-1 ligands, and fragments thereof which also inhibit TREM-1, small molecules inhibiting the function, activity or expression of TREM-1, siRNAs directed to TREM-1, shRNAs directed to TREM-1, antisense oligonucleotides directed to TREM-1, ribozymes directed to TREM-1, aptamers which bind to and inhibit TREM-1, fusion proteins between human IgGl constant region and the extracellular domain of mouse TREM-1 or that of human TREM-1.
 4. The method of claim 1, wherein the TREM-1 inhibitor is administered in combination or alternation with a JAK inhibitor.
 5. The method of claim 4, wherein the JAK inhibitor is selected from the group consisting of CEP-701 (Lestaurtinib), AZD1480, LY3009104/INCB28050 Pacritinib/SB1518, VX-509, GLPG0634, INC424, R-348, CYT387, TG 10138, AEG 3482, 7-iodo-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine, 7-(4-aminophenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine, N-(4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)acryl amide, 7-β-aminophenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2amine, N-(3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)acrylamide, N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine, methyl 2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidine-7-carboxylate, N-(4-morpholinophenyl)-5H-pyrrolo[3,2-d]pyrimidin-2-amine, 7-(4-amino-3-methoxyphenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine, 4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide, N,N-dimethyl-3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide, 1-ethyl-3-(2-methoxy-4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)urea, N-(4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)metha-nesulfonamide, 2-methoxy-4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenol, 2-cyano-N-(3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl-)phenyl)acetamide, N-(cyanomethyl)-2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidine-7-carboxamide, N-(3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanesulfonamide, 1-ethyl-3-(4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)-2-(trifluoromethoxy)phenyl)urea, N-(3-nitrophenyl)-7-phenylthieno[3,2-d]pyrimidin-2-amine, 7-iodo-N-(3-nitrophenyl)thieno[3,2-d]pyrimidin-2-amine, N1-(7-(2-ethylphenyl)thieno[3,2-d]pyrimidin-2-yl)benzene-1,3-diamine, N-tert-butyl-3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide, N1-(7-iodothieno[3,2-d]pyrimidin-2-yl)benzene-1,3-diamine, 7-(4-amino-3-(tri fluoromethoxy)phenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine, 7-(2-ethylphenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine, N-(3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)acetamide, N-(cyanomethyl)-N-(3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanesulfonamide, N-(cyanomethyl)-N-(4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanesulfonamide, N-(3-(5-methyl-2-(4-morpholinophenylamino)-5H-pyrrolo[3,2-d]pyrimidin-7-y-1)phenyl)methanesulfonamide, 4-(5-methyl-2-(4-morpholinophenylamino)-5H-pyrrolo[3,2-d]pyrimidin-7-yl)benzenesulfonamide, N-(4-(5-methyl-2-(4-morpholinophenylamino)-5H-pyrrolo[3,2-d]pyrimidin-7-yl)phenyl)methanesulfonamide, 7-iodo-N-(4-morpholinophenyl)-5H-pyrrolo[3,2-d]pyrimidin-2-amine, 7-(2-isopropylphenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine, 7-bromo-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine, N7-(2-isopropylphenyl)-N2-(4-morpholinophenyl)thieno[3,2-d]pyrimidine-2, 7-di amine, N7-(4-isopropylphenyl)-N2-(4-morpholinophenyl)thieno[3,2-d]pyrimidine-2, 7-di amine, 7-(5-amino-2-methylphenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine, N-(cyanomethyl)-4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)benzamide, 7-iodo-N-(3-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine, 7-(4-amino-3-nitrophenyl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine, 7-(2-methoxypyridin-3-yl)-N-(4-morpholinophenyl)thieno[3,2-d]pyrimidin-2-amine, (3-(7-iodothieno[3,2-d]pyrimidin-2-yl amino)phenyl)methanol, N-tert-butyl-3-(2-(3-morpholinophenyl amino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide, N-tert-butyl-3-(2-(3-(hydroxymethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)-benzenesulfonamide, N-(4-morpholinophenyl)-7-(4-nitrophenylthio)-5H-pyrrolo[3,2-d]pyrimidin-2-amine, N-tert-butyl-3-(2-(3,4,5-trimethoxyphenyl amino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide, 7-(4-amino-3-nitrophenyl)-N-(3,4-dimethoxyphenyl)thieno[3,2-d]pyrimidin-2-amine, N-(3,4-dimethoxyphenyl)-7-(2-methoxypyridin-3-yl)thieno[3,2-d]pyrimidin-2-amine, N-tert-butyl-3-(2-(3,4-dimethoxyphenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide, 7-(2-aminopyrimidin-5-yl)-N-(3,4-dimethoxyphenyl)thieno[3,2-d]pyrimidin-2-amine, N-(3,4-dimethoxyphenyl)-7-(2,6-dimethoxypyridin-3-yl)thieno[3,2-d]pyrimidin-2-amine, N-(3,4-dimethoxyphenyl)-7-(2,4-dimethoxypyrimidin-5-yl)thieno[3,2-d]pyrimidin-2-amine, 7-iodo-N-(4-(morpholinomethyl)phenyl)thieno[3,2-d]pyrimidin-2-amine, N-tert-butyl-3-(2-(4-(morpholinomethyl)phenyl amino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide, 2-cyano-N-(4-methyl-3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)acetamide, ethyl 3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)benzoate, 7-bromo-N-(4-(2-(pyrrolidin-1-yl)ethoxy)phenyl)thieno[3,2-d]pyrimidin-2-amine, N-(3-(2-(4-(2-(pyrrolidin-1-yl)ethoxy)phenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)acetamide, N-(cyanomethyl)-3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl-)benzamide, N-tert-butyl-3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)benzamide, N-tert-butyl-3-(2-(4-(1-ethylpiperidin-4-yloxy)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide, tert-butyl-4-(2-(4-(morpholinomethyl)phenyl amino)thieno[3,2-d]pyrimidin-7-yl)-1H-pyrazole-1-carboxylate, 7-bromo-N-(4-((4-ethylpiperazin-1-yl)methyl)phenyl)thieno[3,2-d]pyrimidin-2-amine, N-tert-butyl-3-(2-(4-((4-ethylpiperazin-1-yl)methyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide, N-(4-((4-ethylpiperazin-1-yl)methyl)phenyl)-7-(1H-pyrazol-4-yl)thieno[3,2-d]pyrimidin-2-amine, N-(cyanomethyl)-3-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzamide, N-tert-butyl-3-(2-(4-(2-(pyrrolidin-1-yl)ethoxy)phenylamino)thieno[3,2-d]-pyrimidin-7-yl)benzenesulfonamide, tert-butyl pyrrolidin-1-yl)ethoxy)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzylcarbamate, 3-(2-(4-(2-(pyrrolidin-1-yl)ethoxy)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzenesulfonamide, 7-(3-chloro-4-fluorophenyl)-N-(4-(2-(pyrrolidin-1-yl)ethoxy)phenyl)thieno-[3,2-d]pyrimidin-2-amine, tert-butyl 4-(2-(4-(1-ethylpiperidin-4-yloxy)phenylamino)thieno[3,2-d]pyrimidin-7-yl-)-1H-pyrazole-1-carboxylate, 7-(benzo[d][1,3]dioxol-5-yl)-N-(4-(morpholinomethyl)phenyl)thieno[3,2-d]pyrimidin-2-amine, tert-butyl 5-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)-1H-ind-ole-1-carboxylate, 7-(2-aminopyrimidin-5-yl)-N-(4-(morpholinomethyl)phenyl)thieno[3,2-d]pyrimidin-2-amine, tert-butyl 4-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)-5,6-dihydropyridine-1 (2H)-carboxylate, tert-butyl morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzylcarbamate, N-(3-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)-phenyl)acetamide, N-(4-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)acetamide, N-(3-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanesulfonamide, 7-(4-(4-methylpiperazin-1-yl)phenyl)-N-(4-(morpholinomethyl)phenyl)thieno-[3,2-d]pyrimidin-2-amine, N-(2-methoxy-4-(2-(4-(morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)acetamide, 7-bromo-N-(3,4,5-trimethoxyphenyl)thieno[3,2-d]pyrimidin-2-amine, (3-(2-(3,4,5-trimethoxyphenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanol, (4-(2-(3,4,5-trimethoxyphenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanol, (3-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanol, (4-(2-(4-morpholinophenylamino)thieno[3,2-d]pyrimidin-7-yl)phenyl)methanol, N-(pyrrolidin-1-yl)ethoxy)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzyl)methanesulfonamide, tert-butyl morpholinomethyl)phenylamino)thieno[3,2-d]pyrimidin-7-yl)benzylcarbamate, N-(4-(morpholinomethyl)phenyl)-7-(3-(piperazin-1-yl)phenyl)thieno[3,2-d]pyrimidin-2-amine, 7-(6-(2-morpholinoethylamino)pyridin-3-yl)-N-(3,4,5-trimethoxyphenyl)thie-no[3,2-d]pyrimidin-2-amine, 7-(2-ethylphenyl)-N-(4-(2-(pyrrolidin-1-yl)ethoxy)phenyl)thieno[3,2-d]pyrimidin-2-amine, 7-(4-(aminomethyl)phenyl)-N-(4-(morpholinomethyl)phenyl)thieno[3,2-d]pyrimidin-2-amine, N-(4-(1-ethylpiperidin-4-yloxy)phenyl)-7-(1H-pyrazol-4-yl)thieno[3,2-d]pyrimidin-2-amine, N-(2,4-dimethoxyphenyl)-7-phenylthieno[3,2-d]pyrimidin-2-amine, 7-bromo-N-(3,4-dimethoxyphenyl)thieno[3,2-d]pyrimidin-2-amine, N-(3,4-dimethoxyphenyl)-7-phenylthieno[3,2-d]pyrimidin-2-amine, and pharmaceutically acceptable salts and prodrugs thereof.
 6. The method of claim 1, further comprising the co-administration of a) at least one each of an adenine, cytosine, thymidine, and guanine nucleoside antiviral agent, or b) at least one additional antiviral agent selected from the group consisting of non-nucleoside reverse transcriptase inhibitors (NNRTI), protease inhibitors, fusion inhibitors, entry inhibitors, attachment inhibitors, and integrase inhibitors.
 7. The method of claim 5, wherein the nucleoside antiretroviral agents comprise two or more of: a) (−)-FTC or 3TC, b) TDF or TAF, c) ABC or EFdA, and d) a NNRTI, a protease inhibitor (PI), or an integrase inhibitor (IN). e) a fusion inhibitor with two nucleosides or and PI or IN.
 8. The method of claim 7, wherein the NNRTI is Sustiva, the protease inhibitor is Kaletra, or the integrase inhibitor is Raltegravir or Elvitegravir.
 9. The method of claim 4, wherein the TREM-1 inhibitor, and the at least one each of an adenine, cytosine, thymidine, and guanine nucleoside antiviral agent, or at least one additional antiviral agent selected from the group consisting of non-nucleoside reverse transcriptase inhibitors (NNRTI), protease inhibitors, fusion inhibitors, entry inhibitors, attachment inhibitors, and integrase inhibitors, are administered in combination.
 10. The method of claim 4, wherein the TREM-1 inhibitor, and the at least one each of an adenine, cytosine, thymidine, and guanine nucleoside antiviral agent, or at least one additional antiviral agent selected from the group consisting of non-nucleoside reverse transcriptase inhibitors (NNRTI), protease inhibitors, fusion inhibitors, entry inhibitors, attachment inhibitors, and integrase inhibitors, are administered in alternation.
 11. The method of claim 3, wherein the JAK inhibitor is

or a pharmaceutically acceptable salt or prodrug thereof.
 12. The method of claim 3, wherein the JAK Inhibitor is

or a pharmaceutically acceptable salt or prodrug thereof.
 13. The method of claim 1, further comprising the co-administration of a macrophage depleting agent.
 14. A method of treating or eradicating an HIV infection, comprising: a) reducing viral loads in a patient by administering a combination of HAART and a TREM-1 inhibitor as claimed in claim 1, b) systemically depleting macrophages with a macrophage depleting agent while maintaining HAART and TREM-1 inhibitor therapy until a sufficient amount of macrophages are depleted, as determined, for example, by flow cytometry that a low level or no macrophages are present in the circulating periphery upon blood draw, c) withdrawing treatment with the macrophage depleting agent, while maintaining treatment with HAART and the TREM-1 inhibitor, where withdrawal of HAART and/or JAK inhibitor is executed upon sustained low level or absent viremia, and d) either withdrawing HAART while TREM-1 inhibitor therapy is maintained, or withdrawing both HAART and TREM-1 inhibitor therapy, optionally while monitoring viral rebound.
 15. The method of claim 14, wherein the macrophage depleting agent is Boniva or Fosamax.
 16. The method of claim 15, further comprising the administration of a JAK inhibitor selected from the group consisting of

or a pharmaceutically acceptable salt or prodrug thereof.
 17. A method of treating or eradicating an HIV infection, comprising: a) reducing viral loads in a patient by administering a combination of HAART and a TREM-1 inhibitor as claimed in claim 1, b) administering a reactivation agent, while maintaining one or both of HAART and TREM-1 inhibitor therapy, c) withdrawing treatment with the reactivation agent, upon assessment of increased viral loads in the periphery that may be coupled with but not limited to assessment of diminished or absent memory lymphocytes with flow cytometry, while continuing treatment with HAART and one or more TREM-1 inhibitors, until low level or absent viremia is maintained, d) withdrawing HAART, while TREM-1 inhibitor therapy is maintained, or withdrawing both HAART and TREM-1 inhibitor therapy, optionally while monitoring viral rebound.
 18. The method of claim 17, wherein the reactivation agent is panobinostat.
 19. The method of claim 17, wherein the treatment regimen further comprises the administration of a JAK inhibitor selected from the group consisting of

or a pharmaceutically acceptable salt or prodrug thereof.
 20. A method of treating or eradicating an HIV infection, comprising: a) reducing viral loads in a patient by administering a TREM-1 inhibitor as claimed in claim 1, and b) administering an anti-HIV vaccine and/or an immunostimulatory agent before, during, or after the TREM-1 inhibitor is administered.
 21. The method of claim 20, further comprising administration of HAART along with the TREM-1 inhibitor.
 22. The method of claim 21, wherein the HAART comprises the co-administration of: a) at least one each of an adenine, cytosine, thymidine, and guanine nucleoside antiviral agent, or b) at least one additional antiviral agent selected from the group consisting of non-nucleoside reverse transcriptase inhibitors (NNRTI), protease inhibitors, fusion inhibitors, entry inhibitors, attachment inhibitors, and integrase inhibitors.
 23. The method of claim 22, wherein the nucleoside antiretroviral agents comprise two or more of: a) (−)-FTC or 3TC, b) TDF or TAF, c) ABC or EFdA, and d) a NNRTI, a protease inhibitor, or an integrase inhibitor.
 24. The method of claim 23, wherein the NNRTI is Sustiva, the protease inhibitor is Kaletra, or the integrase inhibitor is Raltegravir or Elvitegravir.
 25. The method of claim 22, wherein the TREM-1 inhibitor, HAART, and vaccine or immunostimulatory compound are administered in combination.
 26. The method of claim 21, wherein the TREM-1 inhibitor, HAART, and vaccine or immunostimulatory compound are administered in alternation.
 27. A method for treating infection by a Dengue virus, comprising administering a TREM-1 inhibitor to a patient in need of treatment or prevention thereof.
 28. A method for treating infection by a Chikungunya virus, comprising administering a TREM-1 inhibitor to a patient in need of treatment or prevention thereof. 29-31. (canceled)
 32. A composition for treating HIV, comprising a TREM-1 inhibitor and a second anti-HIV agent, along with a pharmaceutically acceptable carrier or excipient.
 33. The composition of claim 32, wherein the second antiviral agent is selected from the group consisting of JAK inhibitors, macrophage depleting agents, nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors (NNRTI), protease inhibitors, fusion inhibitors, entry inhibitors, attachment inhibitors, integrase inhibitors, anti-HIV vaccines, immunostimulatory agents, fusion inhibitors, macrophage depletion agents, and reactivation agents.
 34. The composition of claim 33, wherein the NNRTI is Sustiva, the protease inhibitor is Kaletra, the JAK inhibitor is Jakafi or Tofacitinib, or the integrase inhibitor is Raltegravir or Elvitegravir.
 35. The composition of claim 32, wherein the TREM-1 inhibitor is selected from the group consisting of TLT-1-CDR2 (SAVDRRAPAGRR, SEQ ID NO 1), TLT-1-CDR3 (CMVDGARGPQILHR, SEQ ID NO 2), LR17 (LQEEDAGEYGCMVDGAR, SEQ ID NO 3), LR6-1 (LQEEDA, SEQ ID NO 4), LR6-2 (EDAGEY, SEQ ID NO 5), LR6-3 (GEYGCM, SEQ ID NO 6), LR12 (LQEEDAGEYGCM, SEQ ID NO 7), prodrugs thereof, conjugated versions thereof, deuterated variations thereof, analogs thereof comprising non-naturally occurring amino-acids, functional variations thereof including a different sequence of amino acids but which retain TREM-1 inhibitory activity, analogs thereof in which each amino acid can be, individually, a D or L isomer, and combinations of L-isoforms with D-isoforms thereof, wherein the peptides can optionally be stabilized by micelles.
 36. The composition of claim 32, wherein the TREM-1 inhibitor is selected from the group consisting of NF-kappaB inhibitors, MicroRNA 294, human cathelicidin LL-37, the F-c portion of human IgG (AdTREM-1Ig), antibodies directed to the TREM-1 and/or sTREM-1 or TREM-1 and/or sTREM-1 ligands, and fragments thereof which also inhibit TREM-1, small molecules inhibiting the function, activity or expression of TREM-1, siRNAs directed to TREM-1, shRNAs directed to TREM-1, antisense oligonucleotides directed to TREM-1, ribozymes directed to TREM-1, aptamers which bind to and inhibit TREM-1, fusion proteins between human IgG1 constant region and the extracellular domain of mouse TREM-1 or that of human TREM-1. 